I'll answer your questions in reverse order if that's okay.
In terms of the picker, if I recall correctly, the reason Suk's mod is incompatible with YNAEMP is that they both edit the same UI files for the game set-up screen. Unfortunately, even if I were to make a mod that just does the color selection drop down, it would probably also conflict with YNAEMP (and Suk's mod of course). UI modding is also something I've never done before, sadly.
Re: Original palettes; that should actually totally be doable so long as you can find the original color's RGB codes (which I think might on the wiki if you look through old versions?). You would just need to add those colors to the database and give them a name and then you could insert the new color names into the second table in Prismatic. The game would still check to see if colors were conflicting so you'll still see some secondary jerseys if, for example, Poundmaker/Trajan/Gilgamesh are in the game, however.