Your backbox lights are on a separate circuit from the Game Over and Tilt lights.

Check your Jones plugs as its intermittent. My klondike was doing the same thing and it ended up being dirty jones plugs.

I can reference my klondike to help you.

Also, you say the score motor keeps running even though the score reels reset to 0. Does the ball eject into the shooter lane and the motor just continue to run? Or does the ball never get ejected over?

So with the tilt and game over lights...they are separate from the back box lights in regards connection in the circuits.

Backbox lights to my understanding (6.4v) are not wired to any relays other than the "lock" which is triggered by pushing the left flipper when power switch is first turned on. I assume all your playfield lights are working (the ones that are always lit under the plastics). All these are fed from the 6.4 side of the transformer into the "lock relay" and out from there on switch to the plugs onto the playfield and backbox.

If they tend to go out during game play I still wonder if its a loose/dirty connection in the jones connectors. As the solenoids are popping during game play the connections may move just to cause the lights to go out.

If the game ends. Do the backbox lights come on again? How about if the ball drains but its not end of game?

This may also explain the ball count unit going out of wack. The ball count unit is in the backbox if i'm not mistaken. So if the connector looses connection at certain points then the unit does not trigger ball count events.

When you power on the game and add credits. Does the ball count light work...should be with 3, 5 or 9 depending on how game is setup.

Just a heads up that the a majority of problems with these klondike/yukon games is in the game over latch relays. They are pretty touchy and if the latch is a little off then the game does weird things. However, it should not affect the backbox attract lights but will screw with the "game over, game in play" modes.

Lots of questions here but I'm sure with some guidance you'll figure it out. People like curriedog and rolf_martin are a wealth of information. They've helped many (including myself) thru the most complex problems.