If your model is in the following list you can change the software via "flash load". I don't know what it costs anymore but used to be around £100. [list=1]UMF003 - 900ss 1998/9, Slip-on Mufflers 
 UMF005 - 900ss 1998/9, Slip-on Mufflers and Modified Cam Timing 
 UMF007 - 900ss 1998/9, 944cc kit, DP cams,valves, Slip-on Mufflers 
 UMF013 - 900ss 2000, Slip-on Mufflers 
 UMF015 - 900ss 2000, Slip-on Mufflers and Modified Cam Timing 
 UMF021 - 750ss 1998/0, Slip-on Mufflers 
 UMF031 - 750ss 2000, Slip-on Mufflers 
 UMF043 - Monster 900ie 2000, Slip-on Mufflers 
 UMF045 - Monster 900ie 2000, Slip-on Mufflers , Modified Cam Timing 
 UMF051 - 900ss 2001, Slip-on Mufflers 
 UMF055 - 900ss 2001, Slip-on Mufflers and Modified Cam Timing 
 UMF061 - 900ss 2002, Slip-on Mufflers 
 UMF065 - 900ss 2002, Slip-on Mufflers and Modified Cam Timing[/list=1] 
 Have a look here: 
http://www.fuelinmoto.com.au/fimnews.html#FLA  You may have to replace your ECU with a programmable one in which case the power commander is the less expensive option. I'd definitely get the mapping checked as these bikes tend to run lean to pass emissions. Speak to someone like Nelly (on this board) who know a lot more than me. 
 [Edited on 28-3-2006 by Felix]