I have a 2000 fatboy. I have tried 2 differnt types of exhaust on this bike and niether fit right. I first tried V&H long shots then the Hooker longs and both installs resulted with the same thing. The bottom pipe which is for the front cyclinder sticks out past the upper pipe. The mounting bracket for both sets was really difficult to get the bolts into the holes. It would have chaulked it up to the pipes but on both sets the bottom pipe sticks out further than the top. Has anyone seen this before? any ideas?

 

When I reinstalled my pipes after a cam install they did not fit right. Took me a couple tries to get the front flange to seat correctly into the head and head gasket. Had an exhaust leak until taking them completely off and trying again a "couple" times. The rear exhaust frame bolt mount did not line up correctly either. It took some patience and a little muscle with some finesse to get them back on. Now that I think about it, and a lunch break!

May not be the same problem as you - sorry of this is no help.