On a related mileage note about the swap, I may see increased mileage soon.
I've been fighting charging problems and random electrical gremlins since shortly after I started driving it daily. In stock form, the PCM acts as the voltage regulator. It was having trouble keeping up with just the headlights and heater fan, and if the alternator cycled off for more than a few seconds at idle the PCM would freak out and completely shut down the charging circuit. I went through and cleaned all of my grounds (or so I thought), without making any difference. I eventually tested with two different used alternators, and one new one, then swapped to an external solid state voltage regulator.
This regulator worked for about two weeks, then all at once my tach needle started jumping all over the place, and all of the lights and accessories would constantly pulse with the regulator. The whole time, the voltage behavior never changed, swinging clear from almost 15v down to 12.5 depending on RPM and the pulsing of the alternator. I went through and cleaned the connections again, filed the battery clamps down, so they'd clamp tighter, and added a ground cable from the top alternator bolt to an existing ground location on the frame. This seemed to help for about a day, then it went back to the previous behavior, bringing us up to this weekend.
This weekend I made a trip to visit family, about 120 miles each way, and on the other side of a mountain pass. While over there, the pulsing became worse and worse, until cars actually started thinking I was flashing my headlights at them! AGAIN, I went through and cleaned all of the connections, then I swapped back the regulator duties back to the PCM, which wasn't pulsing as badly, so I could get home. Other than the annoying pulsing the drive home was uneventful, but when I started it to drive to work on Tuesday morning I noticed a loud squeaking noise from the engine compartment. Upon inspection, I found that the lower alternator bracket, an off the shelf GM F-style bracket, had snapped. I'd been trying to chase down a rhythmic high pitched squeak at idle since I started driving it, and apparently it was this bracket flexing against its self!
Tired of messing around, I had a full set of large gauge welding wire battery cables made, and acquired some mil-spec battery terminal clamps. Over the past two days I have completely rebuilt my alternator bracket, and replaced all of the cables. The alternator bolts to the top of the engine mount, which it did before, but now the bracket is PART of the engine mount, constructed of the same heavy steel and fully integrated instead of add-on. The mount is STOUT now!
I did not remove the charging harness when I did the engine swap, because the cables are harnessed together, and it wasn't necessary for clearance. When I removed the whole thing this time to replace the harness I found a large ground cable that I had somehow missed, hiding behind the engine wiring harness on the firewall. Doh! The location is such that when the hood is lifted, all of the great Seattle weather that has built up in the gap between the hood and cowl runs down right over the bolt. When I removed the bolt, I found all sorts of pretty green, red and white colors!
I went through, and used a small wire wheel to make all of the cable bolts and mounting surfaces shine, then used some anti-seize when connecting all of the new cables. Result? Success! The lights are bright, even at idle. Turning on the headlights, or accessories barely makes the needle twitch, and it's locked solid at somewhere around 14.5v. The pulsing is completely gone, and my oil pressure reads about 20% higher (it uses the common ground).
Additionally, there is an unexpected benefit. The engine is MUCH less labored! Idle is significantly quieter, and normal acceleration and cruising are easier, showing 1-2psi less boost during these conditions. The boost still responds instantly to the same levels as before when pulling a hill or getting on the throttle. I've figured out that the connection was so bad that the regulator was running the alternator at 100% most of the time before! I'm hoping this will also help give me a bit of a boost in mileage as well.