Getting South, Then Working North.

That's do-able with about 20 days (it'll be a little tight), but I think you have a couple non-trivial issues...

Generally: Your proposed timing makes sense, you will just need to ensure ferries are running when you need them. When high season ends, ferry availability plummets, some routes have less frequency, some routes just stop running entirely. My guess is that you would be OK in early September but by mid-September, things could get trickier. You'll need to check this carefully, as one missing ferry line could make your plans collapse.

Generally #2: Much (most) of this region is best done by car - ferries help, but there's little rail service. There's some bus, but it's often not efficient nor convenient for tourists. The big issue is getting dinged for picking up a rental in one country and dropping it off in another.

Fly into Dubrovnik - that's your starting point, no? For Kotor, just rent a car for the day locally - it's easy. We arranged our car through the owner of the flat we stayed in. Ferry to Korcula, then Hvar, then back to the mainland at Split. Rent a car there, head up the coast to Zadar, Plitvice, Istria. Drop your car there (Rovinj can work for that).

You'll need to figure a way to get across the border by public transit (there's a bus/van to Piran/Portoroz - check this very carefully, bus may be full if you're just waiting to hop on and there may not be another for a day or two). Get a car for Slovenia once across the border. We did this (in reverse order) and it worked fine.

Fly out of Ljubljana - unless you want to spend time in Venice, why go there? Both Dubrovnik and Ljubljana are well served by international airlines (easy one-stop connections to USA through Frankfurt). Split, Zagreb and other cities also have flights.

I would start with flight logistics because that will be your limiting factor. I have flown open-jaw to Croatia several times. I consider into Dubrovnik and out of Zagreb to be the ideal scenario, but you have many options to scope out.
Some meandering thoughts:
Fly into Dubrovnik. If you arrive early enough, you can try to get to Kotor that day by bus, but since all that after overnight travel can be exhausting, we used a private transfer. If it's just Kotor you are interested in, you could consider doing a day trip. A lot depends on how many days you prefer to spend at your first stop. Kotor is tiny, so a night could do it.
Dubrovnik is also quite small, and it gets inundated with cruise passengers, so again not a lot of time is needed here (I am generally not a fan of lots of 1 and 2 night stops, but this is a long trip--I would balance by picking somewhere at the midpoint to stay several days.)
You can get to Korcula by bus (bus takes a ferry) or catamaran. The two main boat operators are Krilo (catamaran only) and Jadrolinija (cat plus ferries for cars and passengers). Check our their websites to get a sense of schedules and routes. (I'll note here that most Croatian islands are quite hilly--I am a bike commuter, but it was too much for me.)
After Korcula, a catamaran will get you to Hvar. From there, it's cat or ferry to Split. Trogir is just a short bus ride away.
At this point, I would determine how many days you want in each of the above places to see what you have left and how you want to proceed. I would be at about my halfway point, but you may prefer a quicker pace.
From Split, it's an easy bus to Zadar. You could do a day trip to Plitvice or stop there en route to Zagreb, particularly if Slovenia is in your ultimate plan. If you prefer more island hopping, I'll ruminate on that below.
I have not visited the Kornati islands, so consult a guide book on that part. I know from Zadar you can get a ferry to Losinj (check schedules as they are limited). Losinj and Cres are connected by bridge and a bus route connects them. I might leave Krk out because you have a lot and I would want a car because the bus-ferry connections get iffy.
From Losinj/Cres, you could continue by bus or catamaran to the Istrian mainland. A lot would depend on your departure point.
I think you have a lot to mull over--feel free to ask more or just mull over your options for a while. It's never too early to look at flights though. Pula and Zadar are options to at least check out.
Here is just a really random sample to work on the day-allotment issue. Without knowing the pace you prefer (I travel really slowly and never cover as much ground), it is hard to advise on number of days. These are minimums:
Kotor 1
Dubrovnik 2
Korcula 2
Hvar 2
Split/Trogir 2
Zadar 1
Plitvice 1
Since we can't put it all together yet, here is the minimum I would want in your other locations:
Losinj/Cres 3 (no there isn't more to see/do here, I am accounting for travel time and transport logistics.)
Rovinj 2
Venice 3 (check ferry schedules at Venezia Lines)
I basically think you could do the northern islands and Istria OR head into Slovenia. Neither is a bad choice.
If you go with a car, renting in Zadar and returning somewhere in Istria would work--you won't need it in the south at all.
Good luck!

I would start by flying into Podgorica, then to Budva for a night or two (Stari Bar and Ulcinj as a day trip) then up to Kotor Bay with only a few hours in Kotor along the yay. It's nice, but if you are going to Dubrovnik you will find Dubrovnik to be a much better version of the same thing. Then the night in Perast, see the 2 islands (couple of hours), and on to Dubrovnik .... I dont like driving on vacation so I rented a car and driver for 70 euro/day. Montenegro is very affordable.

If you are travelling in September, you would be better starting north and heading south weather wise.

So you will have 18 days on the ground? Day 1 will be lost to jet lag and the last day is just getting to the airport, so that’s really 16 days. Drop Venice as it is too far out of the way and Ljubljana. Fly open jaw into Zagreb and out of Dubrovnik. Spend a week in Istria covering the hill towns and coast - ideally hire a car as this is the easiest way to get around and driving is easy there and then spend a night at Plitvice before heading to Split where you should return the car. Split itself needs at least a full day and Trogir another.

Head to the island of Hvar for 3 nights - if you aren’t into partying, Stari Grad or Jelsa would be quieter options. Then head to Korcula for 3 nights. Many places on the islands have a 3 night minimum booking. Head to Dubrovnik as your final stop and go to Kotor as a day trip.

The previous posters have given solid advice and have more recent island experience than I do, so I just have a few things to add:

I think your original list of islands is awfully long. I like islands and I'm sure those are all lovely, but I think they will become somewhat repetitive and you will reach the point of diminishing returns before you hit the end of the list. And traveling to islands sucks up a lot of time. I've only been to Hvar and Rab, so I can't help you winnow the list down.

In theory, you could fly into Podgorica, the capital of Montenegro, and travel by bus to Kotor to begin your trip there. Alas, the most interesting thing about Podgorica is its name. But Montenegro is beautiful, and just about any bus trip will be interesting. Not really recommending this, just mentioning it.

Between Dubrovnik and Kotor is the town of Herceg-Novi, which is much less touristy than the other two. It's worth a few hours of wandering around, which you might have available if you happen to hit a mega-cruise-ship day in Kotor and don't want to spend the full day there. Kotor is very nice if there is no monster ship in port; otherwise, it's very crowded and loses a lot of its medieval atmosphere. (So check the ship schedules online before planning your day-trip to Kotor).

One disadvantage of driving between Dubrovnik and Kotor is that I suspect your ability to fully appreciate the magnificent fjord-like scenery will be diminished by the need to keep your eyes on the road. I don't think a bus is a terrible option here, but that's the only way I've traveled that route, so I can't compare it to driving.

I would not skip Plitvice, which is arguably the best destination in Croatia. But you must spend the night before your visit in or near the park so you can get in at opening time and beat the day-trippers. It may help a bit to go midweek, if that is possible. A lot of the other visitors on the Ausgust Friday I was there seemed to be Croatian. There is bus service to the park from Spit (perhaps via Zadar--I haven't checked) and from Zagreb, but a car will definitely be helpful in traveling efficiently to and from the park. A car also opens up the possibility of staying in a small lodging outside the park; a few may have transportation to the park, but I'm guessing not too many.

I have found the BusCroatia website pretty reliable, but my philosophy is that the only information that really counts is what you get at the departure bus station. So verify everything when you arrive in each town. Tourist offices can be helpful on logistics if you hit them when they aren't too busy. I noticed that, rather than checking bus schedules online, they picked up the phone and called the bus station in the departure city. I figure they have a reason for doing that. I highly recommend buying cross-border bus tickets early. In my experience those buses head out rather full, and I'm sure they sometimes sell out completely.

There are good bus and train links between Ljubljana and Zagreb, which is a very interesting city and a nice change from all your coastal destinations. I think the travel time is no more than about 2-1/2 hours. I believe there are more buses than trains.

In 2015 I was able to take a bus from Ljubljana to Rovinj. It may have run just once a day, but it was very useful.

I like your plans. From Dubrovnik, you can take the catamaran ferry to Split. It stops at Korcula and Hvar. I did not inquire as to getting off on Day 1 and back on on Day 2 or 3. That's probably an option. The complete trip D-S is about 4 hours.

As to bus travel in Croatia, we used Flixbus last summer, and found it convenient, inexpensive, and satisfactory. In 2014, we tried to take the bus from Mostar to Dubrovnik, but this was Oct 31, and the buses were closed down for the winter. In September, I would imagine they are running a full schedule.

I do agree with acraven. I'm not 100% sure that hitting all the islands is necessary. Many say that Hvar is over the top as a drinking destination for European youth. This may be an interest of yours, but possibly if you want a less intense party atmosphere, other islands might be better.

Car travel in Croatia is easy. There is a main autobahn-like superhighway. There are smaller roads. It's easy driving there.

Thanks for your replies. I was out of town this weekend so couldn't respond right away.

I know I don't need to hit all of the islands but find myself most interested in views of the sea from smaller coastal towns - medieval preferably. I'll probably read your comments on islands five or six times to ferret out which are best bets and which could be skipped.

I'm thinking the loop into Slovenia would be with a car rented in Croatia and returning in Croatia to avoid the big drop charge. Essentially, I'd see the two Slovenian stops as part of a loop with a rental car. If Zagreb is good to fly out of, I may return the car there before flying home. Zagreb isn't really high on my list so I didn't mention it here but it's not out of the question either. I would like to see Venice again, I've only been once, in mid October a number of years ago with family in tow, and really enjoyed it. If the trip is too tight, however, it's the first thing I'd drop. The second thing I'd drop is Slovenia and make it part of another trip.

I flew back to Washington-Dulles from Zagreb in 2015 with just one stop somewhere in Europe (maybe Frankfurt). It was very easy. Zagreb isn't watery (no river downtown, unlike Ljubljana), but its historic area is very nice, and it has many good museums--I think more than any other city in the Balkans (ignoring Greece here).

Postponing Slovenia so you can see more of the country on a later trip would not be a bad thing, in my view.

Don’t make the mistake of thinking that the whole of the island of Hvar is like Hvar town - it’s like chalk and cheese. Most posters on this forum don’t seem to have been anywhere other than Hvar town and have judged the whole island from that experience!

The catamaran heading north from Dubrovnik runs in the late afternoon, arriving in the evening. You can get off at any island, but you would have to buy another ticket to get back on. Many places on the islands have a three night minimum stay. The catamaran heading south from Split runs in the morning.

You may want to consider Krka NP rather than Plitvice, which is stunning and has fewer crowds.

What can I expect for air and water temps in second and third week of September?

Google water temperature with the name of a coastal town.

I'm currently using the Timeanddate website for historical weather data, since wunderground has been flaky for me recently. I've linked to Dubrovnik's data for September 2018. You'll need to scroll back a bit to find the middle of the month. You should go back a few more years so you have a reasonably accurate feel for the range of what you might experience; the website has ten years' worth of data. Then repeat for your other destinations.

If you want to look at some averages to figure out the best route, you can often find those on a city's Wikipedia page. I am bothered by the fact that the period on which those averages are based cuts off at 2010; weather has gotten more extreme since then.

I don't consider averages sufficient for planning travel in general, but mid-September will probably be very nice throughout the area you plan to visit. The one issue I have with that month is that the days are getting noticeably shorter, and I'm one of those people who needs sun for energy.

We were just in Croatia from September 8-22. We had gorgeous weather— sunny and warm every day and nice ocean temperatures. Obviously that is only one year.

In terms of islands, look at Vis. It was our favorite place in Croatia—absolutely beautiful and undeveloped, because it was used as a naval base until 1989. No ugly Communist era buildings. Mamma Mia 2 was filmed there. From Vis, you can take boat tours to the Blue and Green Caves.

If you time it right, you can take a catamaran from Hvar to Vis. (I believe it only goes 1 day a week). We liked Stari Grad much better than Hvar town and wished we had stayed there.

Thanks for the comments on the islands, they are really helpful. Timing ferries to make good use of them without long delays might be tricky.