Barbara has reported many of the large museums in Zagreb were still closed at the time of her most recent trip due to earthquake damage. I haven't checked their current status. Perhaps two nights there (at the beginning of your trip, so probably only one non-jetlagged day) might be sufficient for you. It wouldn't be for me, because it's a beautiful city with an atmospheric, bi-level Old Town and a bunch of small museums that, at last report, seemed to be open. In particular, check out the small but choice Museum of Naive Art and the very popular Museum of Broken Relationships.
I spent several nights in Rovinj and enjoyed Istria a lot. I took public buses to Porec and the little coastal village of Vrsar, then I took a once-a-week bus tour to inland Istria. The tour went to Motovun, Groznjan, Pazin (the capital) and a winery.
I think one night at Plitvice would be completely adequate for most visitors who arrive by mid-afternoon and can do part of their park exploration then, as others are leaving. However, I imagine you can fill a full day plus a few hours by going beyond the plotted-out walking routes. I'll just mention that as of 2015, the posted walking times seemed really conservative. I beat them easily, and I was dealing with massive crowds of fellow day-trippers throughout my visit; that definitely slowed me down. If you aren't at all tight for time, by all means allow an extra night at Plitvice. I love the place (have been there three times), and I would use that night elsewhere. Coastal Croatia is full of attractive towns.