So, to wrap it up. I put 600 kms on the sled since I installed the new stator, no problems, runs great. I even put the old battery back in.
Since I had the engine out (yes...you have to gut the whole sled to get to the stator, only thing left was the track):
replaced the plugs
changed the engine oil and filter
changed the in gas tank strainer
changed the inline gas filter
changed the anti-freeze
changed the brake fluid
overhauled the driven pulley. Two of the rollers were broken, weird. This might explain the burnt drive belt smell I often had.
replaced the driven pulley countershaft large bearing. It was shot. That eliminated the annoying high pitch hissing noise when riding. Good thing, I thought it was a bad bearing in the gearcase.
Also replaced those silly pop rivets they have all over with bolts and lock nuts.
Total: $840 CAD in parts and $200 CAD in labour (had the shop overhaul the driven pulley, didn't have the tools).
This is funny: