Go over all the data cables. They go board to board according to the attached chain. Red is data out, green is data in, so red feeds green from board to board. Follow the chain along, look for where in the chain the blinking starts and it will be either the last board lit solidly or the first board that's flickering where you will most likely find the problem. No matter what, NEVER plug in or unplug the violet and black power connectors with the game power on - you will blow things up - however it is perfectly okay to manipulate data cables with the power on.
WoZ C-52_Cable Routing - Copy (resized).jpg