1st thought was that somebody got you and sold you a bike with a swapped frame or motor but. Gen 2 guage cluster? Have you looked over the harness yourself for splices etc? Check the oil pan? Doesn't sound right. I'd get a 2nd look or opinion.
Some things aren't worth the trouble and or your life. I'd spend my money on something that is either made for my bike or has hundreds of people who can vouch for it, done it and test it. It's not a seat, decals or paint. These are wheels and on a motorcycle that's everything.
Curious why you went through the trouble of changing the forks/trees for the conversion? You could have left that alone. Besides that now you can catch a Gen 2 for 5k to 6k. I did it a few years back and for me...it wasn't worth the time and energy.