Anyone else using MegaSquirt on a LA motor?

No not at all. Unless there is excessive shaft play. I think the root cause of the problem is really the low rotor speed and the number of internal coil windings of the VR. Try what you can, also inspect the teeth for anything ther than sharp, clean edges. No chips or heavy scratches. I’d think for you to get it to work you’d need a different, more powerful vr pickup and a matching toothed wheel setup.

Try configuring tunerstudio per diyautotune.com using a vr pickup. Also try the pull-up resistor. And of course, adjusting the resistor pots on the board.