make sure all your plugs are plugged in. there is a ton of them, and it's easy to miss one, or get one trapped under the board and be out of sight.
also, try rebooting the machine while holding down the service button (the one on the IO board that you have to press to bring up the operator manual)
and see if the game boots to give you the option to reload all the software. this will let you know if the game is properly detecting the IO board.
if it does not, you have probably plugged a cable on the motherboard into the wrong place. there is a 12 or 14 pin connector that is essentially a serial connection to the IO board. there is a few spots on the motherboard it can slot into, but it only works with one. i don't remember what happens when you plug it into the wrong one, but it certainly doesn't work. i outline the sockets with plugs in them with white paint so i know which one goes where.
if it does boot up to the reload screen, give it a reload and see if it smartens up.