Well I think I've got this odd problem solved...

I took out the engine last night to (at the very least) seal the thing up. After sealing it up, I inspected the flywheel/CB. One of my clutch springs broke... Odd, never had that before... So, I take it all apart, and after much fussing, realized that the brass taper-cone that the flywheel sits on was about 2mm too long. When I tightened up the bolt that holds the flywheel down, it wasn't exactly holding the flywheel in place rigidly. With a load on it, the flywheel would spin freely. This caused a lot of friction generating a ton of heat, not to mention the "no load" effect it had on the engine.

So, fixed it up, and I'm looking forward to getting it broken in today. Another 2-3 degree day today. Perfect!

Thanks for the help DJ.