Did some more work on the car and got it to a point where I could drive it around. It drives wonderfully, there's a nice deep power well on it that's easy to tap. Still have a bunch of things on the to-do list though.
Yesterday I said the belt was riding on the back of the pulley and rubbing on the water pump housing and we concluded that the crank pulley was the problem. Today we brainstormed about it some and decided that it couldn't be the crank pulley, since it has a high enough torque that the bolt is forced to sit flush on the crank snout, and besides, all that stuff is original to the 4.9 block so none of it is different (not intentionally anyway). As a lark, we put a hardened washer in the crank pulley as a spacer, and with the bolt tightened down the belt does clear the water pump housing by a hair, but not a lot. Looking at things a bit more, I remembered that the water pump gasket was the thick fiber gasket that came with the AC Delco pump and not the thin paper type, and that may be contributing to the problem a little. Also, looking at the water pump pulley that I am using (which came from the donor 4.9) it appears that the belt has been riding off the rear of the pulley for a while, so maybe the stamped sheet metal pulley is just pulled in a bit and the belt is naturally riding off the back of it, which is worsened by the thick gasket. Long story short, we will try swapping on the pulley from my 4.1 tomorrow and see if the belt still gets sucked in towards the housing, if so we will look at replacing the water pump gasket with the thin paper style. As of right now, with the spacer in the crank pulley, the belt is not rubbing against the housing, but the crank pulley is free to walk in towards the snout so it might later.
Power steering leak was just the high-pressure fitting hadn't been tightened. Easy fix.
I had a vacuum leak in my cruise control, probably the vacuum switch on the brake pedal is holding the vent open but I don't care right now so I blocked off vacuum to the solenoid and will deal with it later. It's interesting how slowly the reservoir builds vacuum pressure. If I start the car then shut it off, some of the interior diaphragms get pissy and start flapping. The brake booster also takes a little longer to build up pressure.
Anyways once the vacuum leak was fixed I was able to set the ISC and TPS. I did it the simple way, removed the ISC from the car and drew the pintle back, then set the idle stop screw to 500 RPM while the ISC was still out of the car. Then I set the TPS to throttle angle zero so I could ignore all of the reference voltage crap, and then put the ISC back in the car and set the gap. It idles and runs good, and I have been having fun tearing up the highway by the shop in my tests.
I still need to set the base timing and replace the water pump pulley at the shop, and then can bring it home. I will fix all of the small little problems like cruise vacuum here.