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If all you did was wire the lower pop bumper coil backwards then it shouldn't have damaged the MPU board. It probably killed the driver transistor Q2 on the solenoid driver board and the diode on that pop bumper coil. Oh the 1 amp slow blow fuse under the playfield near the flippers probably should have blown too.

Check the white-blue wire from the lower pop bumper switch that goes to two 30 point rebound switches and down to the outhole and left outlane. You might have a break in that daisy chained wire connection at one of those switches.

If you currently don't have a battery to the MPU board or it's flat, that may explain the random credits on power-up.

The 5 amp fuse blowing on the rectifier board is a concern. Make sure on the bottom of the playfield the fuse near the flipper mechs is a 1 amp slow blow and hasn't been overfused in the past.