EFI Bung in head update

Being as it wont loop back would tell me that it is something in your MS hardware. Check all solder points to make sure that nothing is crossed and all diodes/capacitors are facing the right way. If you've desoldered anything make sure that the solder pad on the PCB hasn't come up as can happen. Even if you bought one of the prebuilt boards I'd check this stuff first since a reversed capacitor or diode is a fairly easy mistake to make.

Really great project you're doing. I'm a huge fan of JB Weld. As long as the mix is right it will remain pretty darn strong. I've seen vids of people fixing cracked blocks with it, with variable results. Be really interested to see how it holds up over tie in the head.