No smoking guns, but there were a couple signs that the motor was getting old. 3 of the 4 pistons had noticable scraping on one side of the skirt, and the rod bearings looked to be pretty worn too. I don't have the expertise to really make a diagnosis, but I suspect the rebuild is coming none too soon. I'll try and get a few better pics of the worn bits up tomorrow in case anyone wants to throw in their $0.02.
I still need to dig into the head and intake mani... those are other possible sources of weird noises.
Also, if anyone has any good info on cleaning engine parts, I'd appreciate it. I want to get the head spotless inside and out, and I'd also like to get things like the alternator and stuff cleaned up nicely before I put things back together.