I have that exact same rifle and literally nearly exact same setup as I had mine threaded and shoot it suppressed as well as I have a Leupold on it but mine is a Vari X III 4.5-14x40AO.
On mine one of the best things I did for it was throw that thin, basically sheet metal, POS bottom metal piece away and replace it with a much thicker one from DIP Inc.
https://www.diproductsinc.com/Detail.aspx?PROD=1511067&CAT=5628
I could never get any consistent torque on the action screws because that thin factory piece would just start bending so I replaced it with the much thicker piece from DIP Inc. I run mine around 20-22 in.lbs in the front and 15-18 in.lbs on the rear one.
Also, and they all seem to have different characteristics so yours may be different but when I give my barrel a good scrubbing my 93/17 HMR always takes nearly a box of ammo before it settles down and will group worth a damn. On mine, until the barrel gets fouled a certain amount it just kind of scatters them all over. So if you do give yours a good scrubbing wait till you've got 25-50 rnds through it before you condemn it. Oh, if you do decide to give the barrel a good cleaning make sure and get some cleaner in the barrel before you attempt to push anything through it. Can't speak for other but when mine is dirty it's a real mother to get those first couple of wet patches through if I don't drip some cleaner in there first.
None of the above may help a darn thing but at this point you've got nothing to lose except your time.
As a last resort you can call Savage Tech support 1 (413) 568-7001. They're usually good about trying to help people sort things out and if nothing works they'll even send you out a prepaid shipping label so you can send it back on their dime and they'll take a look at it, but, since your barrel has been altered from stock and threaded that may void their help. If nothing else works I'd still give them a call and see if they'll do anything to help you out.