Bringing the post back from the dead: I always run searches and find that the OP usually doesn't follow up on the outcome of the issue. I'd like to follow up and let whoever may be in my shoes in the future know what happened.
I ended up sending the rifle back to Savage with a pretty lengthy letter outlining the steps I had taken to come to my conclusion that either the barrel was not relatively square to the receiver or the mounting holes weren't drilled parallel to the rifle bore. I got the rifle back last week (about 4-5 weeks after sending it).
They sent me a brand new rifle (different serial numbers) complete with new magazine and picatinny base. In the box there was a 12" target with a hole in the top, bottom, left, right and center showing full range of windage and elevation adjustment as well as a target with a 1.2ish" 3 shot group at 100 yards. I wasn't all that impressed with the group but thought "whatever." I removed the factory EGW 20 MOA base and behold, the receiver had been marked with a pencil around the scope base holes. Somebody obviously read my note and double checked this. I cleaned it and installed my Ken Farrell 20 MOA base, TPS rings and NightForce scope. I got off work this morning and headed to the range.
I convinced myself that the market was short on ammo and components these days (and I was tired after my 12 hour tour and it was pretty cold, wet and windy) so I only shot 6 shots. The first was a cold clean bore shot I deemed a flyer after seeing where the following two impacted. I made a quick adjustment and laid down a quick 3 shot group which ended up being 0.600" on the nose at 100yds. I was using the "el cheapo" factory 250gr Sellier & Bellot ammo. I know I could have adjusted a tad more to get perfect but this morning was about confirming I had a decent rifle. I'm pretty confident I could do better with some hand loads and sun shinier weather.
I think Savage Arms did a good job of making the customer happy in this instance. I was initially skeptical being this was my first Savage rifle but I am excited to know that I can start developing a load without worrying if my rifle can shoot. Savage could have better kept up with communication as I never received a phone call or email and it could have been faster but all in all, it looks like things turned out ok.
I did take my first elk/bull on my Colorado Elk hunt at 420 yds with my .300WSM too. I really wish I would have had the .338 Lapua up but everything worked out. Not an obscenely far shot and not a huge bull (still a trophy to me) but I was tickled pink to fill a tag on public land.