I fitted the full Staintune system to my RT a couple weeks ago. Before that, I installed the Staintune full system to my "old" R1200GS.
The best way to do it, is to start with the headers. Make sure you buy new exhaust gaskets from the dealer.
Put on the new gaskets.
Screw on the headers... but DO NOT tighten them down. Just lightly screw them in.... enough to be able to move them.
Spray some silicone, or WD-40 on the ends to be fitted. It just makes it easier to slide on.
Connect everything, including the muffler... but make sure you don't tighten *anything*, until everything is in place.
Once you're happy with the way things line up, go ahead and tighten things from the headers on, then clamps, and so on.
