Find someone with a '99 cylinder and stock '99 pipe and swap them, or have your '98 cylinder ported for low end and find a used '99 pipe on an auction site.
I had a '99 CRE I bought from a former district enduro champ and it was SWEET off road. Great trail bike/enduro motor.
Factory Connection can do a great job with your suspension, BTW.
Motor mods to my '99 were an e-line lighting coil (acts like a flywheel weight but even better), v-force reed block, '97 carb and ignition, FMF Turbine Core spark arrestor/silencer. Stock '99 cylinder and pipe.
Riding my buddies '05 KTM 250 EXC back to back, the motors felt like twins. Excellent low end for a 250 2t. BTW, I ran a 49t rear sprocket in all but the nastiest stuff, and then used a 50. With the 49, you shift less and can hold 1st and second longer.