Remove the innerconnect board and look for cracked solder joints on the header pins. If these are fine then check the aux power supply for the same issue.

Does your aux power supply board have zero ohm resistors on it or metal jumpers?
If it has zero ohm resistors then lock on a non working coil in coil test, then take a jumper wire and place it across each board jumper one at a time and see if the coil fires now.

Take a pic of the board.

Have you replaced F-4 yet. I have seen a fuse look and test good but when power was applied it would open up and not pass any current.

Some system 11 games the programming cycles the AC relay in attract mode and some don't. When you do the TIP ground test it stops cycling because you have it energized. Now if you had done this to a power coil it would have burnt a fuse, you should have only briefly touched the ground jumper and then it would have clicked on an off. Now you need to test for voltage on both sides of the f-4 fuse while in coil test for one of the non working coils. Somewhere there is a bad connection on the power side of the non working coils. All the affected coils have the same 50 volts on them. It can be the AC relay points are bad on the 50 volt side. This is hard to test properly.

I did not know you had J12 disconnected. You need to look for a shorted TIP36a on the aux power supply. It will correlate to one of the non working coils.

Then remove 1J11, 1J12 and 1J19 from the cpu board, install 5J12 on the aux p/s and install a good fuse in F-4. Power up and see if the fuse burns now.

With the game on in attract mode check all 22 solenoid Tips for ground on the metal tab.

I mean check the resistance to ground with an ohm meter. Any thing below .600 meg is a problem.