Raptor winter maintenance.

I am going to do the 50 conversion as well as the v2 frame upgrade.
What all should I be checking/replacing, greasing while I have her frames split?

-Bearings for notchiness, shafts for signs the inner bearing races weren't spinning on the them. Bearing spinning on shafts can be stopped with the use of green Loctite. This stuff is pretty much permanent and if any of it wicks into the bearing you're screwed.
-Make sure your fuel tank doesn't have any places where screws were trying to poke through. This is a good time to replace the clunk line in both tanks. If you're going to v2 frames you will need a different main tank anyway. Just replace the factory clunk line in the new tank with the black Hayes tubing before installation.
-You should consider getting the third bearing kit from the SE since you are running a 50 now. You can check it now to see if your pinion gear is getting beginning to mesh cockeyed against the main spur gear. Uneven spur gear wear will be visible. I was going through a start shaft and pinion every season before adding this kit. The v2 frame upgrade requires changing to the v2 start shaft, bearings and clutch assembly anyway.
-Thunder Tiger makes an aluminum post upgrade I would recommend whicb really stiffens the frames. I went to these on my very first Raptor. Still using the same set.

There really isn't much in there beyond that.