I posted a reply to one of your earlier questions about a stay in the Dolomites, but let me expand on my comments, since your planned route aligns so closely with a trip my wife and I made this past August and September. We spent 24 nights, with stops in Ortisei, Verona, Modena, Trieste, Rovinj, Motovun, Baska on Krk Island, and Zagreb. We have also visited most of your Slovenian sites and Plitvice on two previous trips. Here's my thoughts on your current plan.
I like the idea of picking up a car in Venice, keeping it for the whole trip, and returning it in Italy. However, make sure to pick it up on the way OUT of Venice. Also, be sure to let the rental company know that you intend to drive in Slovenia and Croatia. It may involve an additional charge, but it's better to be up front about it then to have to buy the car if you have an accident in a country where it is not insured. And don't forget to drop into your local CAA to get your International Driving Permit. I assume you plan on flying back from Venice, but a flight from Verona is worth looking into. And speaking of Verona, I'd recommend staying there at least three nights- four would be better- and visiting Padova as a day trip by train. I don't know if your kids would be into it, but watching a opera under the July night skies in Verona's ancient Roman arena is a once in a lifetime experience!
In Istria, we split our time into two spots. There's really no need to do so- I'd recommend hunkering down on the coast for your whole time in Istria, and day trip. We loved Rovinj! You are fortunate to have the luxury of four weeks to travel, but even so I would not push as far south as Zadar. As beautiful as it may be, it makes for a very long trip to the area you want to focus on and puts you in the car for most of two days instead of on the beach where you should be in July. Even more true if you plan to visit the rest of the Dalmatian coast on a future trip.
When we stayed in Ljubljana a few years ago, we did two day trips by car- one into the Julian Alps, including Kobarid and the Vrsic Pass, and the other in the Karst area, including the Skocjan cave and the Lipica stud farm. Both were full days, but entirely manageable. (We had previously stayed at Bled, so didn't go back there.) Ljubljana makes a great base, and five nights there would allow you time to see all the places you list. If you want to cut down on the return driving though, spend a three or four nights in Ljubljana, and three at Bohinj, with a day trip to Bled from there. (If you weren't planning on spending time in the Dolomites, I would more enthusiastically recommend a stay in Bohinj.)
Consider making Tre Cime a stop en route from Slovenia to your stop in the Dolomites, rather than doubling back on a day trip. As for the Dolomites, I have not visited Cortina, but it is close enough to Ortisei to visit one from the other. If you want more detailed info about the places we visited and stayed, feel free to private message- information is useless unless it's shared!