Sean: I took the crank gears off, so it wasnt them. I've also been starting with the two 13mm nuts and then doing the correct tightening order on the main crank nuts.
One of the biggest things that helped to fix the tightness was to put the oil pump in ... which didnt occur to me for quite a while, but it seems to push the case out quite a bit and let me torque those last two crank nuts (closest to the pulley) down to spec without locking anything up. In addition to the oil pump, the permatex is taking up some space and allowing me to get the proper torque readings without locking anything.
I think I'm all set now. Still scared because I'm not used to how things "feel" but I'm told that I'm being paranoid and that a loose crank would be worse than the way mine is now.
Since I torqued the rest of the case flange nuts, the crank is tight-ish again, but I dont know how to describe it. It takes quite a bit of force to get it moving, but then it moves smoothly. I am moving it by hand with the flywheel. I've spoken with two machinsts, and they both think it feels fine, so I'm going ahead with the build. I'm done pissing and moaning about it.
-biggie