I've done two runs today in coming back to this game and my hands (mainly wrists) are absolutely killing me from the constant controller shaking I have to do. I generally don't experience this with any other games. Anybody else experience this/know anything that can help?

Dont shake up and down aggressively. slight flicks in the proper direction will do the trick for any motion control. If you are just returning from not playing for a while. It might take a little bit of time to get used to relaxed motion.