It turns out it was a couple of different issues. I don't know what caused what, but the OS in the "rebuilt" IP from Heath was bad and we had a section of burned wires in the wiring harness (buried in the harness). I have no idea what caused the burnt wiring. There were no blown fuses and it was obvious by the corrosion on the bar wire that it had been that way for a very long time.
We installed a new pump (thank you Advance Diesel in Anchorage for the new pump) and I repaired the harness and we finally got the thing started on Friday. I tuned it the best I could, but it still has a light stumble at idle and just off idle, but going down the road it runs nice and smooth with good power. I wish I had time to get it 100% correct, but I had to catch a plane early Saturday morning.
Concerning the TDC offset reset and setting the IP timing, I simply couldn't get things right. I went through the reset procedure a few times, but I simply could not get the value down below 1.9. Obviously, that is way off the -.25 to -.75 mark. So, I tried setting the timing (as it says to do in the manual), but I couldn't get the actual pump timing (as read on the scanner) below 9ish. Again, way off the 3.5 mark. I did get the IP timed to the point that the scanner would read 3.5, but the motor ran terribly. So I did the TDC offset procedure again, then the IP timing read 11ish without touching the IP timing.
Having run out of time, I had to leave it the way it is, but I'd love to know your thoughts on why I can't get the TDC offset and the IP timing within the correct values. My best guess is that it's a timing chain issue, as a few of you mentioned above.