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).