It looks like you and the folks chiming in have done some pretty good troubleshooting.
I really doubt that Clive would have implemented the 5V regulator resistor hack (step 42 in the PinWiki). Clive is a solid tech from what I hear.
Have you repinned the female connector at J101 and J129?
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Chris Hibler - CARGPB #31
http://www.Team-EM.com
http://webpages.charter.net/chibler/Pinball/index.htm
http://www.PinWiki.com - The Place to go for Pinball Repair Info