Twdy, I highly recommend you stick with the Dyna muffler and make it work.. you will not find a better one for $100, and you got this one for free?
You've been given some good advice here and I can't add much, except that a couple of washers will help the rear mount and muffler rail go from near-perfect to perfect alignment. It is true that the header collar will not butt against the muffler. There is about an extra 3/8" of header behind it that doesn't matter, especially after you fit a heat shield. It's also true that you should put some copper shim stock between the header and mufflers to make the english and metric stuff match diameters. It also helps to cut a couple more relief slots in the muffler (go from 2 to 4) and put a washer behind the lower mount of your
front heat shield, loosen the header collar at the cylinder and swing the header outward slightly.
I know this sounds like a pain, and the "it's a direct bolt on" claim is somewhat exagerated. But gee-gads! I just spent almost $400 on a whole exhaust system specially made, artisan-welded and all that for another bike, and it didn't fit as good as the Dyna on the Savage. You gotta tweak stuff no matter what you do