When I did the 99s, I started with 400 grit, although I wasn't trying to sand off paint. The clear coat was peeling like crazy. Yes, they would need to be re-cleared if you don't want to continually wax them.
I think I stopped on about 1000 grit and then started polishing them with various compounds.
I also took apart the headlight to do this.
The headlight before was not cleared either. I told the buyer they would need to wax them about once a month or have them cleared themselves.
This was the before: