i also agree with scott on the factory procedure -only because if done like the factory this question wouldn`t arise. BUT...in looking at the paintwork which looks amazing i can see the show benefits of painting things apart-we do it when customers want show type finish-what do we do for the bolts-get yourself another set of new bolts-blast them and dip them in a good thin etching primer then spray them with the same paint color-hopefully direct gloss and not clear over base. let the paint harden and get yourself the snap-on sockets that are lined in rubber to prevent paint chippping-i`m sure you can get 7/16 1/2 and 9/16. that will cover most of your bolts.
good luck
all the best
frank.