Lets start with basics. Have you checked the barrel to make sure nothing is touching? I have never seen a chassis where this is needed but I don't keep up with the chassis market at all. Have you taken the rifle apart to verify everything is lined up? Have you checked your bedding work? Have you tried shooting it without the muzzlebrake or with the factory one to see if that is the issue? Can you verify barrel twist? I don't know, I doubt, that savage may have some how put the wrong twist in your barrel and that is the issue.

I am not a fan of cannons like this, but it is rare to find a Savage that doesn't shoot right out of the box and rarer to have problems after everything you have done.