The paint looks great. It's going to be a beauty for sure.
The rear wheelwells do look a little large for that wheels and tire combo.
Have a look at Jason Osborns's site and you'll find some of the nicest resin wheel/tires combos availaable IMHO, only as a buyer.
I don't know the status of this build but as far as your paint problems go, you did say "Tomorrow is a couple more coats and some clear before I start decals."
If that means you put a couple of coats of colour and also clear on the same day, (and 3 different clears) that might just be the problem.
Just a thought as I'd never do colour and clear on the dame day.