So after some more reading and testing, I decided to ditch the GoodSets and use No-intros because the box art, snaps, and the like all use the same naming convention.
I decided to create some X-Arcade Tankstick CP skins to modify some of the various CPs displayed via GameEx, CP Wizard, Xpadder, and the like. I will provide the Adobe PSD and Gimp XCF files once complete. Here are a few examples: I have created Adobe PSD and Gimp XCF files for ease in creating some X-Arcade Dual CP skins as well as provided an example of a KOF skin. xarcade_tankstick_overlays.zip xarcade_dual_overlays.zip
This is an excellent call (IMO). In doing so you also ditch a bunch of bad dumps, alternate dumps, etc. GoodSets were fantastic in their time, and even still serve as a good archival tool consisting of 'all known dumps', but in terms of playable sets they really are a bit antiquated at this point (IMO once again).
You can do it all manually by going into Setup Wizard>Custom>Advanced Emulator Setup then simply choosing whatever paths you already have but I have to also strongly suggest EmuMovies for all artwork. It does cost some money but think of it as a long term investment, and for it you get a program which only asks you for your roms folder and then a place to store ALL the artwork and it does the rest of the work automagically. After it all gets downloaded you only have to tell GameEx where those paths are and thats it.