Ok, hmmmmm....somethings to think about,
1) Remember that when you sit on the bike the swing arm changes angle, so you will never get a straight line up to anything other than the header pipe.
2) The stock muffler is shaped funny so to make anything line up like that will be a real task.
3) many people use Sporster mufflers and they sometimes need the angled pipe. Sorry , not sure why, could be the mounting brackets.
Suggest trying a muffler shop to bend the pipe..
You will need to do the following to get the "right" angle (pun intended): Get a piece of household wire (12-2 works good), then have someone sit on the bike. Line up the muffler how you think it looks best. Support it some how (blocks of wood, old books, piles of magazines). Then stand back and look at it. Do a walk around too. Once you're happy, take that wire and using the centerline of the muffler and the centerline of the pipe, bend it to the angle you need. Muffler shop can work from there.
Good Luck. Send Pict's when done