What handlebar options are there for 99 thunderbolt. they are 1/4 inch from the tank and my knuckles hit the fairing.

Well there's the S3T handlebars which are more upright, and I could be wrong but I think the S3's handlebars are 7/8", so any bar of the same diameter should fit. There's also these little spacer things which raise the bar up about an inch or so, other than that I don't know what to tell you.

I've got a 99 S3T, with a 3/4 inch spacer under the stock "T" bars. It is a very upright position with lots of clearance. My first step would be the T bars, or just look around as they are 7/8, BMW R90S bars are nice, as well as Honda CB900F bars.

Good luck