Here is a suggestion you don't want to hear: sell them and build your own from wood.
I purchased an arcade cabinet a while back and the guy threw in a megatouch machine that wasn't working and had no boards. After looking at it for a few months, I finally decided to make a jukebox out of it. Like you, I wished I built from scratch. The end result was good, but I spent more time trying to make the megatouch cabinet work.

Unlike your project, the idea of using it as a jukebox isn't far off from it's original use as a megatouch. Trying to add a keyboard, buttons and a trackball just sounds like too much modding to be worthwhile. I've built about a dozen bartops and I wouldn't consider using a megatouch cabinet again. Consider building from scratch, otherwise Malenkos suggestion of a add-on control panel is probably a decent way to go.