Have you replaced the 0.047uf ceramic capacitors on the various switch matrix switches that use them? The schematics show which switches have caps on them. I've seen a number of Eight Ball Champs lately that had switch issues and the caps were the solution a couple times. I would start there regardless, because they're most likely due for replacement anyway.

Edit: i see you already changed the caps, but you mention you didn't change them all. Personally i would track down the remaining caps and change them. I would double check that all wires and diodes are connected to all switches in the problem rows/columns--a light tug on each wire and diode to be sure they aren't hanging on by a thread. Re-flow the header pins for the switch matrix on the mpu and re-pin the female connector there too.

Excellent!! Good work!

Those caps can fail a couple different ways and sometimes will affect other switches in the same rows/columns, so it's always smart to do all of them on these games. Enjoy your EBC!