All of the motors will bolt up thru '07, it's best if you have the correct ECU for the motor. I think the series was '99-'01,'02-'05,'06-'07 on the ECU.you also should keep in mind the fuel delivery system layout; 2001 thru 2007 has the fuel pump in the tank so this may require some small changes to your hoses.Refer to your Suzuki bible to get the specs;Servicing Information 8-23, will show '99-'00.Section 10-8-5,10-8-6 & 10-8-7 will show 2001-2007 basic layout.If you don't have a Suzuki Service Manual, be sure to get one so that you'll have all of the correct information regarding the motor mounts and their torque specs etc. I've done 4 complete builds,working on my 5th(all busas) and drag race mine every weekend-manual was the best part I've bought.
Hope this helps & good luck