you may have a faulty opto, switch or a bad power connection to several optos.
what it sounds like is the machine is getting a false reading telling it there are balls where there are no balls, so the pin says there are to many balls.

i have not worked on a jp before but you said the power room coil keeps kicking, i would be checking the optos or switches in the power room first as it sounds like it is trying to clear a ball or balls out of there. if the optos in that area have lost power to them or are out of alignment ( if it has optos), or if there is a switch stuck on the pinball machine will just keep trying to clear that area by kicking its coil over and over again.

let me know how it all goes

i would have to look at the schematic and the trex to see what could be causing the switch errors.