Oh joy. Was hoping it would be easy. lol Ahh, nothing ever is...
Now, removing the wheel pants (temporarly, w/o flying) is within the limits of owner performed maitenance, correct. Would assume it is since I would have to remove them to change a tire, right?
You are permitted to remove and install them for the purposes of the tire removal and installation, but operating the airplane with them removed will (legally) require an updated W&B and log book entry, both by an A&P.
Depending on the vintage of wheel fairing, they could be fiberglass or an ABS plastic. You should not use paint stripper on anything but metal parts of the airplane. Wet sand and feather out chips and prime and paint over, you will never notice, especially since you say you are only keeping it about 700 days.
Charles