it is funny, you mentioning these problems. I ran into the same exact problems with my 3" HS downpipe. I used my dremel and widened the holes, and took the downpipe to an exhaust shop, where used a heat and dimple technique to give space for nuts to be installed.
People on the forum say to just hammer the piping, without heating it up. Believe me when I say that it is IMPOSSIBLE to make any kind of real dent (no less, dimple) because of the thickness of the piping. You'll need some sort of torch and a set of rams/dimples if you want to do this on your own.
