Bought a Savage MKII FV-SR a couple weeks ago and have been using it casually at the house for rabbits/squirrels/chipmunks etc. while I wait for my AAC Element II suppressor.

I've heard that the factory stock isn't as accurate as the Boyd's stock.  I've also heard that bedding your stock improves accuracy.

Should I invest the $200 (as much as I paid for the rifle!) to get the new stock and bed it?

Yes boyds

Yessir. My Savage A17 had a synthetic factory stock and I put a Boyd's on it and bedded it. The groups tightened way up and the flyers went away.
My 10/22 with the Boyd's stock was pretty darn accurate and bedding that one even made a difference.