Good to hear it's working. I thought the hall effect pick ups side stepped all of the VR problems. In fact, read through the docs about using the hall sensors. You may need to cut and reroute a couple of jumpers. I don't think the hall is supposed to use the VR conditioner circuits the pots are associated with. I believe the hall sensor should be hooked in where the VR conditioner circuits hook to on the board. You may be amplifying an already amplified signal and causing sync errors. Did the assembled ecu docs say?
And oh yea. Packing 25 or so 16ga wires into a head shell designed for 22ga to 28ga wire takes a little carefully applied force. I'm still tempted (and if any gremlins arise, i will) to buy one of the DB37 pigtails diyautotune offers.
I'm working on getting the rest of my car drivable before I proceed on the tuning. Glad to hear the selftune part works well. I boned up and bought the upgrades for the tuning software, but haven't yet hooked in the O2 sensor. I still had exhaust leaks, so it wouldn't be accurate yet anyway.
Edit. In the megamanual
MegaSquirt - Electronic Fuel Injection Computer by Bowling and Grippo ©2010 Assembly guide (I'm only familiar with V3 that I'm using) for the V3 item #52 you have to select VR OR hall. It tells you what jumpers need to be connected. The hall sensor connect directly to the opto isolator. The hall sensor shouldn't be ran through the VR conditioner where the pots are. The megamanual is a lot to slog through, but check this out.