yeah that is a BIG HUGE OPPS! i remember hearing horror stories of that before whether RGP or marvin 3m. You may want to try and contact Clay, he may have some good documentation or ideas.
i guess you can start by getting the schematics out and seeing what types of lines you crossed. I have a feeling it was some signal lines with power feeds. So you sent power into all the switch inputs.
Also, i remember reading that some games were built with the connector colors the same both black so you had to make sure the same wire colors were on both sides of the connectors.
Well a learning opportunity for sure, not an easy one lots of damage. it is like adjusting pop bumper score switches with power on and then shorting to the solenoid voltage bad things happen.
Not impossible by any means but likely took out several things. Good luck.