A little update to my own issues.

The color issues where solved with adjusting the TV. The games going back to the menu are not an issue with the TV, (duh) I forgot I refreshed the build and probably need to adjust what emulator the rom uses. I'll need to play with the resolutions a bit more to see what looks best, I made some progress with the TV output settings but will probably just run the options remotely through ssh to adjust retropie / emulator settings.

Now if only I could magically shave 50-75 lbs off the CRT! (the things a beast)