Not sure of all the troubleshooting steps you have done yet, but my process would be to start from square one.

For me that would involve:

1) Disconnecting any third party lighted mods just to get them out of the equation. Also the most likely place where the installation could've shorted something.
2) Double and triple check anywhere it looks like something may be shorting against something else if mods don't solve it (sockets, etc. like manadams said).
3) Unplug all of the LED control boards and start from the CPU down, plugging them in in order, seeing of you can spot where things start going wrong.

And lighted barn mod, looks like lighted tower mod as well. I am assuming the game was working and playing fine before the mods were added (otherwise why add them?). Would be the very first place I would start. Would be really confusing why pinball techs wouldn't remove them just as a matter of course until the problem was solved.