Motor swap not as trivial as you might imagine - it's not a difficult job, but more parts than you may think.
I have '02 Daytona motor in my '98 Speed Triple - pretty much same considerations as in your case when swapping to later motor - in addition to list below I also needed to replace the MC1000 ECM and the fender/battery box from later 99-01 model (you won't need these)
Lot's of things to change you may not have considered:
Headers - much bigger bore & with lamda sensor & exhaust (you can't fit 97-01 can on an 02+ header so that has to be replaced also) ;
airbox (airbox is not a straight fit under the late tank so need some mod there);
complete main wiring harness;
Regulator/rectifier & need to custom mount to frame (stator is in the motor, not one piece auto style alternator like earlier motor);
brake rearset (the early will interfere with the exhaust header);
need digital instruments to go with later harness;
use a Sprint Electronic Speed Sender (form & fit in the 97-01 wheel);
oil cooler (different connections) - or would need to have special hoses custom manufactured with the appropriate fittings on each end.;
radiator - the thermostat & sender are in the '02+ motor, so you need to lose the assembly under the tank cowel & create a filler connection - see my gallery for pics of how I adapted my original radiator (although I subsequently replaced with a 1050 S3 radiator).
You also have to 'cheat' the electronics in the ECM for the tank level sender - will throw an MIL otherwise; or else you need to graft a late tank sender into early tank (they are not interchangable -completely different fitment)
Think that's about it - as aforementioned it's a lot more than you may have anticipated!

See some pics in
my gallery