Search for my posts containing the word "MagnaSave".
They cover the overlap between MAME and VP/FP controls and a few simple wiring tricks to combine default MagnaSave and Upper Flipper controls into one flipper button while keeping the related MAME buttons separate.
For the flipper buttons, Goldleafs are way better than microswitch buttons, and leaf-switch buttons like the GGG ClassX True-Leaf Pro are probably better than Goldleafs. (haven't tried them yet, but the reviews look promising)
Another thing to consider is nudging - digital (L/R/Up) or analog.
Scott