See, if you have your crank sensor still hooked up to the stock ECU than all that wiring potentially becomes an antenna for noise.

I didn't have a scope at the time to see exactly what was going on, but when I ran the 3 wires from the crank sensor to just the MS using a shielded twisted pair (because that's what I had available). I ran 8v from the MS to the crank sensor, and used the shield to supply ground (not ideal, but better than no shield at all).

Joel Baldridge, ASE Certified Master Technician, Audi Certified Expert Technician