i've noticed with cars too, some of the same identical cars bone stock, some are faster than others..honestly i think its on the break in of the rings when the engine is fresh....the engine that was babied when brand new seems to be less powerful than the engine that was driven hard off the show room floor, its all in the ring seating...
then again you said the 98 has more compression eh?
you never know the 2001 may be bored or stroked
stock sprockets on both bikes??