I bought the one with 2 holes in it and I think I figured out where it mounts on the trans. The previous owner mounted the rear brake switch to one bolt and a small breather on a bracket to the other bolt. Rather than trying to move them, I just mounted the SE mufflers to the frame with some aluminum brackets I made, and I put a big rubber gromet in one of the brackets. Now the SE mufflers move with the motor when it rocks, and the bike has a lot less vibrations.
I found the Staightshots for the FXR but they show a couple different pictures. One site indicates they are real long and another shows them shorter. I like the shorter ones in the first link and the price is lower, but then the 2nd site has free shipping. Which length of pipes are on your bike and what you're saying V&H gives you all the mounting brackets to attach them to the trans?
http://www.jcmotors.com/pc-5581-1126...fxr-87-00.aspx
http://www.phatperformanceparts.com/...ductCode=16807