I would start troubleshooting this one by swapping the two flipper boards that are mounted on the side of the cabinet. Sometimes the wiring is long enough to just swap the connectors left and right, in other case, simply unscrew the boards and swap them. This is an easy way to check if the problem is on those flipper boards. The opto's (or even their ICs) do get funky sometimes (fluttering) and that could cause the holding power to quickly activate and deactivate, making the coil hot and less powerfull.
Once you have moved the boards and the problem does not move to the other flipper then you have a short on the Fliptronics board. First thing you need to be aware of is that closing your coin door will enable/disable the high power circuits, so make sure to keep your coin door open, you don't want to melt your brand new coil! But don't forget to close it while testing or you will get zero readings (a real "doh! Moment sometimes)
But let's first see what the above procedure will tell us...