I did exactly what you propose for Krka and Skradinski Buk: parked at Skradin. I parked in what I thought was a "free parking" lot operated in conjunction with some local restaurants. They wanted you to buy something or eat at one of them. I didn't really have time, so when I got back to my car, I simply tried to pay the attendant - but they insisted I had to buy something instead! So I went in and bought a soda or something - that's all they needed to see. I would have given them more in cash than I paid for the soda. Oh, well...
I went in May and don't recall if I had to pick a specific boat to the falls or not. I didn't book anything in advance; I simply parked, found the ticket office for the park/boat, bought my ticket, then headed right to the boat, which was leaving. I think it was just first come, first served on the boat, not a timed entry: show them your ticket as you get on, and the boat leaves when it is full or at the scheduled time. Not sure if you can get an advanced ticket or not.
For Plitvice, I would definitely recommend getting to the park as early as you can in the morning - 7am is ideal. There are even some overpriced park hotels that are still super convenient - right in the park, closer to the actual park entrances than the parking lots are (for the parking lots, you park across the highway, cross the road, then walk through the hotel parking lot down to the park at least that's how it is down at entrance #2). Plus, if you visit the park two consecutive days - say one evening and the next morning - the park hotel can stamp your ticket from the previous day so you can enter again without paying twice. The park hotels may already be booked for June, though. But it's worth checking.
