what Pi you using? B+ or 2?
as i think this’ll make quite a bit of difference, as i have a complete theme ready to be released, but its very much a stripped down theme!
now mine is based on a B+ and i have 49 folders all working perfectly (i have that many as i have split most systems up by region) by the looks of it you have lots going on in those theme folders, for a B+ theme, but it should work no problem on a rpi2,
i suggest take what you have but build it again, from scratch or just update it to be used out of the box for retropie, don’t test on other systems, just test on your Pi, as i think you may need to resize some things
but i’m not too sure if ill release it as an updated emulation station should be on its way….