I'm sure you've done it but double and triple check every connector you broke to pull the board, one by one, that it's in the right mate and that it's a good connection. Then look around for things you didn't touch on purpose to see all is as it should be (no broken soldered wire connections, etc). Disconnect the MPU power cable and take readings on the power supply board too, especially making sure you still are putting out a good 5v to the MPU. Also, did you unplug the line cord from the wall prior to pulling the bottom board?

The reason I ask about the line cord is that line voltage is present on the bottom board even when the game is switched off. There's a risk of shorting to ground on any one of the exposed connections (like the transformers) as things/parts are being moving around. But you probably would've noticed that as the spark/flash/noise/smell would've grabbed your attention when it happened!

Still look for a bad connection or broken wire as well as those to the coin door. And check the power supply voltages to verify the MPU is getting the proper 5V it needs to bootup.