Ok, I rescind my theory about the wires on the clip. It must have been that the clip was just loose enough on the chip that barely tapping on the wires was enough to move it... wherever it needed to be.
This is one of the oddest things I've ever observed in electronics. This "wiggling the clip" should NOT work, and why it does has me very curious. I did do some additional testing and observed that by removing either wire from PIN 8 or 4 from the small 8 PIN PCB and then putting them on the PIN loosely and jiggling it, I could get the lights on the MB to respond in a similar fashion, i.e. bright yellow, to dimmer yellow, and occasional flickering red. I bet if we got a petentiometer of the correct OHMS (whatever that would be), we could narrow down what the magic value is to make this work reliably. If I had any, I would test, but I don't.
This time it took me a LOT longer to come up with the magic to flash my other chip. I observed that the lights turned yellow during the verification process, so I thought for sure that it would fail, but it said VERIFIED, (which I didn't believe). But I was able to read the written copies three times, and then I compared the CHECKSUM to the other board flash, and they were identical:
edbbe3cbf8e3fa4a9d991e0681f2a5702b248224
So now I'll put my machine all back together again, and will see if my efforts have been truly successful or not.