Since I just wrestled with installing a new muffler and ran across this exact issue, I'll toss in my experience.  I bought a long megaphone muffler because I wanted somewhat of an old-style look.  That is before I realized the stock muffler angles 5-10 degrees from the header pipe.  The new muffler, if straight, would have ended up through the swing-arm and next to the brake control.

What I did was add a small section of automotive flexible muffler pipe between the header pipe (You can buy this at any auto store in multiple I.D.'s for about $8/ 2 feet) and the "slip-on".  This allowed me to angle the muffler any which way I wanted so I could mate it to the rear.  Then I sealed it to the header pipe with a small wrapping of muffler repair tape, which you have to run about 30 minutes to cure it rock hard.  I didn't seal it to the slip-on because it is enough of a press-fit that it isn't leaking and still allows me to remove it in two pieces.  

This is an "ugly" fix, but I was going to add performance exhaust wrap anyways...which I did, and that covers it all up so no one can tell what I did underneath.