I've researched a couple manuals, and here's what I've worked out thus far.
The secondary 12 volts(unregulated) is generated thus so... The transformer feeds a 9.8volt AC voltage to the power driver board via J112-11,-12). The voltage passes through fuse F116. Then feeds the ac sides of BR-5 (a 35 amp 200V bridge rectifier) to generate 12 volts DC unregulated on the DC sides. And the unregulated 12 volts out put through 3 Jumper plugs (J116, J117, and J118).
Each of these 3 plugs are all supplied by the same 12 volt source.... so logic dictates that something (or the sum of many somethings) is drawing too much current on one or more of these plugs.
J116 supplies the cabinet voltages like the Left and Right Flipper Opto boards and the Voltages for the coin door lights via the coin door interface board.
J117-2 Powers the Dot matrix controller via J606-7
J118 powers the the playfield boards, as well as most of the inner workings of the cannons. It powers the Left and Right EMI boards that ultimately move both Cannons back and forward. It powers the 16 opto pcb which controls most of the optic switches in the guns and optics in the subway tunnels, and the borg entry and lock optos. It also powers the trough optos (both sides). Pretty much anything that needs 12 volts for the photo voltaic LED switches. It also powers the Left and Right proximity switches (or the EDDY switches)
Mine has the added load of of a color DMD expander....but to be fair, I'm pretty sure it was blowing fuses before I installed the DMD expander as a color dmd.
My current plan is to unplug anything I can that won't keep the game from playing and see if that drops the temperature of the bridge rectifier. Like unplugging the EMI boards and disabling the Guns. I might try to get my hands on a loop ammeter and see what the amps each board is drawing. See if the sums of all amps add up to more than the 3 amps of the F116 fuse.
So again, I ask if any of these items that are drawing 12 volts from J116-J118 are more suspect or prone to failure than others.
I did have some issues with subway tunnel optos in the past(IIRC a broken wire), as well as my game registering bad optos on the Borg entry(switch 48) and Borg Lock(switch 31). Although, it could have just been low 12 volts or my crummy playing. Both seem to work in test mode.