Just check the crazykong picture of the pcb, it looks like only two of the rows have roms, the others are empty.
Now I will take a stab at this, I bet I know the reason why this isnt working. If you had the game plugged into the jamma harness, and then powered the board, and THEN put on the TB harness, then you have fried one of the surface mount fuses. If you look at them, they are near the TB harness header. Youll see a set of a few of them, but if one is cooked, the TB wont work.
Look for visibly cooked surface mount fuses. They are so wimpy, doesnt take much to fry them. Now, all you have to do is desolder them, remove them, then just bridge the gap where the fuse was with solder, and it will work again.