You will need to have the ECU reflashed by a dealer (no SLP exchanges on those pipes for the ECU flash )...
Since you are talking about a Y pipe as well... I assume that you are talking about a 2006 900....The two different year pipes are not interchangeable. .... eg cant run the 2006 pipe on the 2005... yes, it will fit, but NO it will not give you the same performance gains. The porting on the 2006's is VERY different from the 2005's. (This is the reason that the 2005 SLP "Performance edition" kit needs porting and the 2006 does not.)
A stock 2005 900 will run more strongly with a 2005 SLP pipe (pn 09-915 ) than a 2006 SLP pipe (pn 09-917).
I was told by Dustin Pancheri at SLP that the 05/06 SLP Pipes themselves are different, the silencers are the same and that the 2006 comes with the Y pipe.
The fuel controller alone will not get the most out of the pipe.... The flash changes the timing and other parameters as well....something the "box" wont do.
Also, make sure that you get the SLP I.D. Card with the pipe... You will need the number on it for the dealer reflash... otherwise, it costs $80 for the new card.