Spook may be on to something about the grounds. The power stages are grounded near the driver side engine mount bracket, the ground tang is secured by one of the bolts that hold down the plastic cable protector that travels across the top of that bracket. I missed that ground when I did the head gasket on mine, it was making intermittant contact while hanging free. The MAF is grounded at the top of the engine with the wires that ground the injectors. Sounds to me like it is either a bad ground or a loose connection. You had to change the big plug at the shock tower for the swap, maybe a wire got crossed or a connection blade got pushed out. Looks like you will have to get the ohm/voltmeter out and spend some hours checking every connection and length of wire. Good luck, let us know how it pans out.

DanR 94 964 264,000 miles (30,000 on the new engine)
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DanR