Matt,
You could put the '06 pipes on the bike - they would mount up the same as previous years. Those pipes might be restrictive enough to richen that mixture enough that the bike would run well. Keep in mind though, that the ECM on your '05 is mapped specifically for the '05 non-catalyst mufflers, whereas an '06 ECM is mapped for the change in muffler. I honestly have no idea how it would run. Only the right muffler on the '06 models have the catalyst in them. That being said, it is more restrictive than your '05 pipe would be. It might just suck even more power from the slightly anemic (in stock form) 88ci engine.
Truth be told, the way the bikes come mapped from the factory, they run so close to too lean for emissions reasons that it is likely the reason yours runs somewhat poorly with any kind of pipe swap and no other mods to it. You can add the highflow setup with the Stage 1 download, but this essentially only alters timing and only takes into account that air filter change. A better way to get that bike to run well is to put either a DFO on it (digital fuel optimizer - think jet kit for an injected bike) or to use a Screamin Eagle Race Tuner to remap the ECM. The difference between these products is A) DFO is a seperate aftermarket component that mounts on the bike, whereas the race tuner just links into the ECM. Benefit of the race tuner is that you dont have the potential for product failure. and B)cost - typically $200 for a DFO, and $460 for a race tuner.
The Race tuner is the best product available to tune the stock ECM, but requires time on a Dyno on top of the product cost to get it setup right.
We have seen very good results with this combination - highflow setup, stage 1 download, DFO, and some type of mufflers/full exhaust system. That'll typically get you a 10% gain in power and torque and get some better sound out of it. Anyway you look at it, the right way to swap pipes is gonna include a high flow filter, a stage 1 download, and pipes and a DFO. The bikes just dont seem to respond as well without all of those components being changed at the same time.
Hope this helps a little. Anything else, let me know.