Wanderer, I think you have a good plan now. And I agree with acraven's strategy for visiting Plitvice Lakes. That is exactly what we did. We purchased 2-day tickets, and selected a 4PM entrance to the park on our first day. We visited the Upper Lakes first. Then the next morning we arrived at the park around 8:30AM and saw the Lower Lakes. If you are early risers and can get there before 8:30AM, that is even better.
BTW, we stayed at Plitvice Miric Inn, if you are looking for a recommendation. It is about a 5-minute drive from Entrance 2. Their breakfast buffet is one of the best I have had. For an additional 20 euros, you can have dinner at their restaurant. It was one of the best meals of our trip. You choose your entrée (we chose fresh trout), and it is served with a huge platter of potatoes and roasted vegetables. The meal also comes with a salad, home-made chicken soup, and the best apple strudel I have ever had. I've heard the in-park hotels are not very nice and the food is mediocre. There are very few restaurants in the area, so you are limited to where you can eat.
If you can, try to spend 2 nights in Zagreb. I think it's an under-rated city. We enjoyed our visit very much. Visually and architecturally, it is very different from Dubrovnik and Split, so it's nice to have some diversity. The Old Town is lovely with 2 different levels, a huge market, and some very interesting small museums.
The train ride from Zagreb to Ljubljana is very pleasant and inexpensive. You cannot buy your tickets online in advance. You have to go to the train station to purchase your tickets.