Adriatic Spin

Maybe consider an itinerary that doesn’t cross the Adriatic. That is, start in southern Italy, make your way north to Venice, then over into Slovenia and Croatia as described, flying home from Dubrovnik or Split or somewhere else in that region. That could work unless you specifically want to do a circle.

Or do as you suggested, flying from Dubrovnik to Bari/Naples/Rome.

Ignoring timing (for a moment) you could start with a "V-shaped" itinerary in Italy, starting in Naples, traveling south and then crossing over to the Adriatic side to travel up towards Venice. Take a bus/train from Venice to Trieste and then travel down through Istria, heading east through Opatija to continue down the Adriatic side of Croatia. In this sequence, Bled is an outlier, which you could travel to from Trieste before backtracking to Istria. Fly out of Dubrovnik or Zagreb, or Ljubljana if you leave Bled for last, though that's really a lot of backtracking.

Having said all that, it is much quicker to get around in Croatia and Slovenia with a car. I used one during each of my Croatia/Slovenia visits to save time over buses. (Normally I prefer trains.) Even with a car, I spent about 4 weeks (over 2 separate trips) in just the Croatia and Slovenia sections of a similar itinerary. I would expect to add significant time if I were doing it via public transit.

I don't love the idea of an overnight ferry trip, but it can't really be that bad--tons of people do it. You can also cross at Ancona-Split. The alternative is to fly, but I don't like flights in the middle of a vacation either. I think the others are on to something with the suggestion to do a horseshoe-shaped trip.
I'd start in Croatia and end in Italy (still good swimming in Croatia, then perhaps slightly fewer crowds and less heat by the time you get to southern Italy). At first blush it seems like a lot even for a month, definitely tight for three weeks. You might cut Vieste--the area looks gorgeous but you are seeing a lot of gorgeous coastline and it is a bit of an outlier (being at least a few hours from the other places).
You might want a car in Istria, the other parts of Croatia mentioned are easy with public transport. I have not been to Slovenia.
Naples area is super without a car; we used one for Puglia twice and would not do otherwise.

I've taken two overnight ferries in southern Europe; one may have been Croatia-Italy, but I don't remember clearly. I found sleeping in a private cabin on a ferry massively more comfortable than sleeping in a train couchette. I wouldn't hesitate to do it again.

I see the merit of a horseshoe-shaped route. We've used ferries many places and the overnight trip didn't put me off. The Drubrovnik-to-Bari ferry just sounded a bit chaotic in many TripAdvisor reviews, in terms of scheduling and crowd control.

I'd thought that by starting off in the Veneto, and then over to Slovenia and the mountains, we'd get the benefit of still-warm temperatures while in the north. And that Puglia and Naples would be cooler and less crowded in October. But that routing may not be possible without a lot of backtracking. (I'm resigned to crowds in Venice whenever we go short of January, but hopefully the back half of September is past the peak of the cruise ship onslaught.)

We may gulp and rent a car in the less-populous and -popular parts of the itinerary. A car has always seemed like an anchor and a bubble to us, and not relaxing transportation. But it was the only way to get to outlier towns in France and served us fine. We'd definitely ditch the car for the Veneto and Naples.

Many thanks for the thoughtful replies.

Driving in Puglia was a complete breeze. If you know how to prepare for ztls and parking, then you have absolutely nothing to worry about. My husband is a good driver and I am a so-so navigator (free data on iphone), so I assist with the traffic circles. There is a lovely coastal drive south of Otranto, and it is nice in the Itria Valley to tool around visiting tiny villages that often take less than an hour to see. I'd only have the slightest pause in high summer due to parking and some coastal traffic.
Lecce could be slightly hairy to drive in and out of, but as long as your parking is set then no worries. You might keep the car as far as Paestum, then drop off at Salerno or Naples airport.

Driving in Croatia will be even easier, and again only really necessary in Istria unless you add more to your Dalmatia section. I did four trips in Croatia without a car and it was just fine, but I can't wait to go back with one. It's one of the places I keep longing for in this pandemic.

Sounds like a great trip--you may have to cut something, but it will still be fabulous.

Is it only me that thinks it is still a lot to do in a month?
I would be inclined to start in Croatia; check ground transport around to Venice, Padova, Ravenna (for something a little different, look at the boat from Venice to Padova through the Brenta Canal visiting Palladian villas on the way....it is an all day trip. There could also be a car trip from Padova to Revenna along that section of the Adriatiac. Some interesting coastal nature reserves and towns off the beaten track.

Alternatively, I would look at flights from Venice to Bari, do the heel and then end in Naples.
As far as cruise ship traffic in Venice, I would expect that if this is for 2021, there will not be full numbers of ships cruising from there, and I notice a number are ending in Trieste instead of Venice. Cruise lines may still be limiting personal travel off of ships for port calls even then. Some are restricted to ship port tours only to create 'bubbles'. Not sure how that will look even in 9 months.
I wouldn't recommend flying out from Venice unless you plan to stay at an airport hotel last night. They seem to leave for the US early in the morning and getting out of Venice (particularly if you prefer ocean travel) is difficult as the first vaporetto leaves later than you would think.

Lots to ponder. Also, lots to trim from the itinerary if we're smart. So easy to over extend when you're sitting at your kitchen table at home, it's snowing outside, and you picture yourself in a 101 other locales. Thank you all again.