My biggest concern is that the original white paint is flaking/peeling off on the hood and windshield header. I'm not sure if I should just sand the areas where it's coming off or what. i don't want the new paint to flake off.
You'll' need to go down to the primer almost on that part, or sand it down all of the way.
I sanded down the bumper covers pretty far because of spider cracks - For the bumper covers I also used "BULLDDOG" Adhesion promoter on it during the process so it flexes a little more and won't chip off. You really don't need a FLEX AGENT for these areas anymore.
You always prime any bare areas - Trust me when I say that the primer REQUIRES the use of a good mask and ventilation.
1) 2 part quartUrethane Clearcoat Kit (catalyst and mixing cup included) 38.70
2) Urethane Base Coat Color. Premixed with proper solvents ready to spray with paint gun., 1992, Mazda, quart, Miata, PT WHITE for a 92 = $74.95
3) 2 part Urethane PrimerKit (catalyst and mixing cup included) $30.60
(The paint code I put in for your car was for a '92 "white" - Not crystal white and probably not the right year for your car either)
This is all quart prices. You could probaly go down to your local PPG store and get OMNI PAINT. Might be cheaper. I got this paint because of the COLOR (RED) - Although the factory paint code for my car is "SU", different comanies make different colors of "SU" RED.