You said the slam-tilt bobber was disconnected, but isn't there at least a couple slam tilt switches. Like on the coin door, and also in the cabinet somewhere or under the playfield? The tilt bob is the tilt mech, not the slam tilt, slam tilt switches are different weighted switches usually on the coin door at least, and or a place or two more. Could there be a slam tilt switch that's not adjusted properly?

Also the DE ball trough is notorious for balls not feeding properly and needing filing smoothing or some people actually put a special insert in there to help the balls roll properly. The switches look normal and adjusted properly to me...

Not sure where/who was selling that trough insert, I never really looked into that. My game does occasionally have a hang up in the trough but it's rare so I didn't try to get the insert, also it raises the balls a bit in the trough and I thought it might mess with the switch adjustment, so I thought it wasn't worth it unless I really was having problems which I wasn't. It's basically a thin piece of thin clear plastic that sits in the ball trough under the balls to help them roll smoothly.
New balls can help, as they can get magnetized after a while, especially some of the super glossy ones, and chromium steel balls. Regular carbon steel balls seem to not have the magnetism issue. If the balls get magnetized they can stick together and hang up in the trough. Anway sounds like you're getting there!

I have the custom 1.13 code installed, which addresses some rule issues, and is a great improvement to the gameplay rules also. Not sure if any issue with the ball hangup issues were addressed in that code though. I still very occasionally get a hang up which flipping the flippers a couple times seems to fix for me. Might look and that #7 switch if it becomes an issue

Just to add some clarification, my game has the original Gun and Smart Missile buttons, and I also have both of those connectors, the one with all the orange wires, printer connector perhaps, and also found the other one with the purple orange black and grey wires not connected to anything. My game works 100% so I can add verification that those connectors are indeed normally not connected to anything. I also have the shaker motor installed and working and those connectors to not have any connection to the shaker. Thought it might help eliminate that as an issue.