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A lot of CDI talk again lately, thought this would be better for future searches. Other members, add what you know so we can all turn back here as a reference point 
My understanding so far is that gen1 and gen2 wiring harnesses can be used with gen1 and gen2 CDI’s. Gen3 can’t be as the plug is completely different.
So, gen1 is 88-92, gen2 is 93-97 & gen3 is 98-00.
How to identify your Cdi.
With the Cdi removed form the machine, stand the cdi upright with the plug facing you.(Edit: plug at the top) 88-92 will have the plug set to the right of the box, 93-97 will have the plug set to the left of the box.
98-00 I have seen two different types, one with wires coming from the Cdi to a plug, wires and plug are a total of around 3”. The other type just has a plug on top of the Cdi. The plug (on both 98-00 types) is noticeably different to the Gen1 & Gen2 varients, a bigger plug, more pins and more square in shape.
Gen1 Cdi’s Have a more advanced timing curve giving a little more throttle response, where as Gen2 and Gen3 have a slightly lower timing curve resulting in slightly less throttle response.
Reputable tuned Aftermarket Cdi’s Are only available to fit Gen1 and Gen2 wiring harnesses, they aren’t made for the Gen3.
Stock replacement Cdi’s are made for all 3 generations.
Gen3 wiring harnesses can be fitted with a 350 Rancher Cdi, power gain results I’m unsure of but being from a bigger CC machine I should imagine there are some noticeable gains.
The only other alternative to getting a tuned Cdi for a Gen3 is to swap the wiring harness for that of a Gen1 or Gen2.
My understanding so far is that gen1 and gen2 wiring harnesses can be used with gen1 and gen2 CDI’s. Gen3 can’t be as the plug is completely different.
So, gen1 is 88-92, gen2 is 93-97 & gen3 is 98-00.
How to identify your Cdi.
With the Cdi removed form the machine, stand the cdi upright with the plug facing you.(Edit: plug at the top) 88-92 will have the plug set to the right of the box, 93-97 will have the plug set to the left of the box.
98-00 I have seen two different types, one with wires coming from the Cdi to a plug, wires and plug are a total of around 3”. The other type just has a plug on top of the Cdi. The plug (on both 98-00 types) is noticeably different to the Gen1 & Gen2 varients, a bigger plug, more pins and more square in shape.
Gen1 Cdi’s Have a more advanced timing curve giving a little more throttle response, where as Gen2 and Gen3 have a slightly lower timing curve resulting in slightly less throttle response.
Reputable tuned Aftermarket Cdi’s Are only available to fit Gen1 and Gen2 wiring harnesses, they aren’t made for the Gen3.
Stock replacement Cdi’s are made for all 3 generations.
Gen3 wiring harnesses can be fitted with a 350 Rancher Cdi, power gain results I’m unsure of but being from a bigger CC machine I should imagine there are some noticeable gains.
The only other alternative to getting a tuned Cdi for a Gen3 is to swap the wiring harness for that of a Gen1 or Gen2.