If you search for TRD Pro Rack removal there is a good thread that covers:
- How to take out the bolts carefully so you don't dislodge the plates (too late I guess)
- How to get access to get them back in place.
- Part numbers for stuff if you have to get new ones.
That all sucks, but I've had the same paint problem and the good news is that it can be fixed, and the roof rack is a hassle but also easy to get back to new.
Good luck!