Thanks for the reply.
It seems that heat was causing the LPE converter to go into protect mode, killing the crank and cam signal. I relocated everything correctly and so far, no issues. EMI could cause issues, like the manual specifically warns, also but would be intermittent. We could reproduce this at will by heating things up, leading us to conclude that heat was the direct culprit.
Still need to change the wires, the EMI coming through the radio is OBNOXIOUS.