'03+ will fit fine, as in '03 the motor was rotated down in the frame 8mm. An older one will fit with a little tweaking. GG OEM pipe, Doma, or FMF. I just ordered stuff from GoFasters last week and they have the new FMF Doma clone pipes, and FMF Turbine Core IIs for the '07/'08s, just came in.
FYI, saw your other post. If you swap your subframe and associated parts to the '07 stuff, you will need an '07 silencer as well or you will need to bend the stinger of your '06 silencer to fit.