Thanks fellas. I appreciate the replies. It appears that I should take a look at IP timing. Seems like an easy thing to check on these engines, and I have the simple tool for locating the reference tooth through the access on the side of the IP. I trust the injectors, and I trust the guy who built them for me. If IP timing were to check out then I would pull the injectors for inspection of spray pattern and pop pressures. Easy stuff first.
The IP in this car is mechanical but the governor is completely electronic, as noted by Diseasel300. There is no diaphragm pod on top if the IP like there is on earlier cars. Here's what it looks like:
And here are the guts inside the governor housing:
And on the IP side:
I lifted those two photos off the WWW but can't remember where. This car's accelerator is drive-by-wire, and because the governor is completely electronic I was wondering if the system has some form of altitude compensation that's not obvious to the eye.
Diseasel300, the crinkly noises I hear do not seem to be associated with one cylinder. Sounds random, but that could be hard to tell at higher RPMs.
Christuna, when cold and the engine is running poorly it's not just at idle. It's bad when moving, too, blowing smoke, bucking.
As an aside, I verified that this car will go faster than 100 MPH. Big rig traffic on I-40 was awful between Santa Rosa and ABQ, and in moment of frustration I floored it to get away from a gaggle that was clogging things up. When I looked at the speedo it indicated 105!