When asking for technical help at the very least let us know the version of firmware you are running.Cliff's Calibration (Mapping) Guide is a MUST READ: http://www.vemssupport.com/forum/index.php/topic,97.0.html
Can't really comment until we see the LM1815 input (pin 3) and output (pin 12) waveforms together, and on a shorter time base like 50us/div.
I think should be better use battery against to the switched supply...
"Coil pack ground separately to chassis"that sounds odd explain more pleasewich ground wire from what coilpack etc