Well one of the rods on my motor is officially toast. I split the cases on my extra motor today to pull the crank and rods out of that one and hopefully they are good and I can use them on the other bike. Still waiting on the machinist to tell me if my jugs/pistons are okay to use.
Splitting the cases turned out to not be anywhere near as big a hassle as I imagined. It took me probably 2 hours on a motor that had been sitting outside for probably 10 years. So my running motor should come apart much easier then that one. Holy cow though, I had no idea those crankshafts weighed that much!