I really appreciate all the replies. I knew I'd get a lot of different opinions, and that's a good thing. I finally got the bike into the shop yesterday, and he was really interested in seeing what had happened. He's still not certain of the sequence of events, but he found the damaged rear cam inner bearing that I knew about. He also found the gear broken in the oil pump and it had spun on the shaft. The heads look good, but the rear cylinder is scored. I'm not ruling out any of the options you guys have shared, and it gave me some good information to talk with my guy about.
Here's some new questions: Why does the HD shop say you can't put a 96 or 103 twin cam A motor in a 2000 touring bike if you can put in a 120R? Is that 120 motor going to be a decent running around town/touring motor, or is it going to get too hot running around in our 100˚ days in the midwest? Is there a consensus on a good, reliable, streetable maximum compression? As I understand it, the 96, 103, 110 have a 4 3/8 stroke. If that's right then would putting a stroker flywheel assembly in a pre 07 motor be less reliable than that same stroke in the later motors. Last, at least for now, with all the talk of having the crank trued and welded does a new crate motor need that same service to be reliable?
Thanks again for all the feedback.