Ok, thanks guys. That different type of wire just looked weird to me and I wanted to eliminate that variable before diving into troubleshooting the switch matrix. I've never tried it before but I found a good video tutorial online so hopefully I can figure it out.
No bad switches show up in switch test so I suspect it is a bad diode causing a signal to leak through the matrix the wrong way.
From what I understand, I have to look for four faulty switches that form a square on the switch matrix diagram.
Currently I am seeing problems with switches "B", "L" and ""O" and "T". Weirdly the diagram does not show a switch B but based on the wiring it must be the one just labeled "S.W."
Now I needed two more suspects, both in the same column and sharing rows with my other problems. I remembered that sometimes my bottom thumper would fire randomly during gameplay. I set about getting it to do it again. I could get it to fire when I hit D.T. #3. Ok, makes sense, it is in the same row. But, then my square would be completed with Top(R) D.T. and I have had zero issues with that. Since the main problem seems to be with the bottom thumper I can then complete the square by going up to (L) Top Slingshot. This makes some sense. Earlier that slingshot was actung weird. It would fire multiple times when hit and then the bottom thumper would go off.
So, I assumed my problem was one of those switches and set out to clip and test diodes. And....of course they were all fine.
While looking at the drop targets I noticed the switch had been replaced on target 2 and the diode was backwards as compared to all the others. Great! I unsolder it, test it, reinstall it the correct way and....no change except that drop target 2 now won't register at all. The replacement switch must somehow be wired different than the originals and need the diode the other way. When I put it back, the switch would again register in switch test.
I clipped a bunch more diodes and tested them including both thumpers/pop bumpers and some other stuff. Everything checks out.
Damn, I really thought it would be one of those given the behavior I am seeing. I need to think about this more.