As though you didn't know, 97 & 98 EV's are odd bikes, in the midst of the transformation from the Cal 1100's to the 99-and-newer models, kind of like a pollywog: Half tadpole, half frog. And they're not all at the same point in the transformation.
On my 98 EV's, the tail light wire connection under the seat is via round rubber connectors. Yours may be like mine, square Molex like the MGCycle part, or something different.
I have left the cable through the fender and pulled all of the wiring out of the taillight assembly on one of mine, and it is a PITA. But so is pulling out the rubber plugs where the taillight cable passes through the fender and getting them back in with the new cable. Your choice of which will make you crazier.
The Third Way is what I did with my customized EV: Cut the plugs off of the the seat end of the cable, and install new connectors after the wiring is fished through the fender. If you have the tools and skills to make good, reliable, weathertight and long-lasting connectors, this is the way to go.