The voltage regulator will need to be swapped out as well.

The VR for a machine with electric start will have a DC output, typically a red wire. That connects to the positive terminal of the battery.

 

I am assuming that the 99 has the e-start. Just use the entire wiring harness. Do you need the shop manual, I'm pretty sure that I have both 97 and 99 manuals. Send me a PM with your email address and which manuals you need and I'll email them to you.

 

the 99 has the Estart I already pulled everything off and the estart wires but dont know where to connect it on my bike to charge. the parts sled is a runner so I wanna keep it running to keep the motor good.

 

the way I understand it that the rectifier makes my yellow ac wire to dc out of the red wire going to the battery correct me if im wrong

 

Rectifier turns ac into dc. DC input to battery is via red wire