At this point I would be replacing U16 - LM339 on the Driver board. This IC is the only IC that is connected to all 4 of the first 4 rows. You should be able to ignore the 4 transistors (Q87 - Q89) and the other 2 IC's (U12 & U13) at this stage.

Hopefully it's just the one chip, and you're back up and running.

Oh goody – board soldering time 
Aaaaaaaaaaaaaaaaaaaaaaaaarrrr – now I am rooted