Claybar usually won't get swirls and fine scratches out. It will take a good portion of the Rain-X off, if not all of it.
There are numerous types of compounds that you can use on paint that are also perfectly safe for the glass. Any type of mild swirl remover or compound and a decent buffer/pad combo will take all that right out. I use it all the time on the glass of my vehicles and friends vehicles to take out waterspots, swirls, etc.
2013 Platinum EcoBoost SuperCrew
Ingot Silver 2WD 3.31
Boss Ultimate | ProComp | Toyo AT2's
Unleashed Custom Tuned
Peragon M3 PTM | BedRug