I've had great help from Cody Chunn, I_Satan and BarakandI on this. The nature of the problem has evolved so I thought I'd summarize in this thread.

Some feature lights work correctly, some do the right thing AND the wrong thing, and some do not work at all. For example: When I start a game, instead of 1000 bonus lit, I have 5X lit. As I manually hit a bonus advance, the multiplier counts down sequentially, and once through the multipliers, the outlanes sequence. If I knock down the drops, the multipliers count up as they should. The Bonus lights do not work at all in test, unless I manually ground them. The back box lights are wacky too, with player up advancing even on a one player game, total players changes during game play, etc...

The problem is found on lamps that are grounded by wires on J1, 2, and 3 on the LDB. All lamps work when grounded with a jumper, and I have run all of the tests in Clay's guide successfully. Everything pulses as it should, and grounding various points on the LDB lights the appropriate lamp. I have an Alltek MPU with the correct dip switch settings for Magic, and have switched in multiple LDBs. The original LDB works fine in another classic Stern. I believe these two factors rule out the boards as a cause. I have matched wires with another working Magic, still no joy. I've searched for shorts on the coin door switches (none) and pulled the wiring harness apart looking for solder splashes that might have bridged wires and found nothing of the sort so far.

So I'm looking for the next great idea for something to check for...or a discount on an exorcism.
Thanks!!

It's a miracle! I cooked up a crazy idea. Thought I'd pull one of the wires on J1 and see what that did to the lights, and see if I could create a variation in the problem and see some kind of pattern. So I pulled the wire to pin 17. None of the feature lights worked, even after I hit the bonus advance a couple of times. So I plugged that wire back in with the power on and noted that I had bonus lights on. WTF?

Powered down and back up, started a game, and all of the feature lamps are now working. So, my conclusion is that through all of my poking, prodding and wiggling of connectors, J1 17 on the LDB never got seated right until just now, thus the game was getting no binary codes for the bonus lamps, and duplicates of the codes for other lights.