I produced a Word doc capturing lots of good discussions in such subjects and just finished going over it again. Bottom line to me is that, yes, variations occurred but that they generally culminated in MORE wheel well parts being painted as production went on, with post war Mustangs starting to see completely painted wheel wells. Prior to that, wing skin surfaces in the wells were left bare aluminum. Forgings, such as the ribs, and extruded parts like the stringers would have seen Zinc Chromate treatment. Some parts would have seen two coats, in which case the second was Green ZC over the YZC. All of this being general of course with exceptions. Variations in finishes were even found on the same plane between left and right wells.
Based on my review, I'm going to take the time to mask and paint the stringers before adding any tubing.
I've attached a pdf version of my file for those interested but it's far from a definitive thesis on this topic. The links may not launch but may be copied to your browser. The canopy animation at the end will not work but the link is provided.