Hi Casey, Welcome to the forum and you gave a great start with information of your situation. As for the bevel, this is a quick shot in the dark as we had another member with a new Hypertherm SYNC machine that was having all sorts of bevel. He had Langmuir and Hypertherm techs involved.
(Edit: His machine was NOT the SYNC version. There is the one outside o-ring that might benefit from grease, but now I am not so certain of my suggestion.)
His solution was to lubricate the o-rings in the torch. A good silicone grease, small amount is all that is necessary.
As for SheetCAM and picking the right offset, here is a post from David (one of our resident geniuses) that answers that: