Sounds like your C2 at the very least is leaking on the original DE power supply, causing low or complete loss of 5volts to the MPU/PPB boards. If it looks wet underneath, that is the issue. All the other smaller capacitors need to changed as well.

You need to measure the 5v, 12v, and -12v. What brand are the boards?

Did you replace the power supply and PPB or they were in there when you got the game?

I think you measure all the coil resistances to see if there are any with shorted diodes, which basically would be any measuring less than 4 ohms.

There should be a fuse on the power supply for 28 volts. None are blown?

No. You can test them with the wires connected.

You had the same problem with the original boards installed? Did you replace both boards at the same time or at different times?

I don't doubt that, but I was trying to see if your issue started because of the original power supply that was installed.

If the coil burned enough for you to see smoke, PIA might be damaged to. I hope not though. If the coil wrapper is not discolored at all then may only be lucky with the TIP122, 2Nxxxx and the 7408. You can use TIP102 in place of the TIP122.

I chased a similar problem for months, and it turned out to be shorted wires. The large wire harnesses bundle (bottom center) was touching a heat sync and a few wires (coil control for me) had their insulation melt and we're shorting to the heat sync. This caused those coils to lock on and eventually blow the fuse. Chase the ghost for a while as if moved the wire bundle while doing diagnostics the problem would sometimes go away.