Chad, I don't know how thick the flanges are on your pipes, but many aftermarket pipes have thinner flanges than the OEM system. Torquing the nuts to the recommended 17ft.lbs. will distort the thinner flanges, and then you end up jamming the acorn nut onto the stud. Some have discarded the acorn nut and used an open nut. Some have buffered the flange with washers. Something I've tried (along with torquing to 15# rather than 17), and it seems to work, is to leave the old, compressed gaskets in place and put the new ones in over them. They seal just fine and that precludes having to use washers or open nuts. Another option, which makes installation easier, is to remove the studs and replace them with Allen or Torx bolts. No nuts to worry about and you don't have to fight the flanges over the studs when you hang the pipes.
Another thing you might want to do is wire-brush the area where your gaskets seat and coat it liberally with anti-seize compound. That holds the gasket in place while you fight the pipes, as well as making it easier to remove the next time. You should also put some on the studs, or on the machine bolts if you do the swap.
