Sounds like you have a lot of noise on the power/ground wires. Instead of using the ignition switch wire harness, for main MS power, use a relay, that is switched on/off from the igntion harness wire, then feed power through the relay from the pos battery terminal. Also, make sure all your grounds are at the same location, and that the ground is GOOD. Maybe even try grounding directly to the neg battery terminal. Also, you can try a car stereo power wire noise filter on the MS 12v Ig wire..

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
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-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)