Flitz metal polish and the Flitz applicator on a cordless drill. Make sure you use masking tape on your sailcloth because the polish will not come off of the sailcloth. I saw this on Truckson Spike a year or so ago and tried it. It works great.
09 Rubicon Unlimited ,3.5RK lift, 35" KM2's with bilstein 5100's,Bushwhacker flats,EVO sleeves and gussets,5.13 gears,trans cooler
Meguires & Novus both make multi-step plastic window scratch removing & final polish kits that are meant for vinyl windows like are in our Jeeps. They start with a coarse grade to get the biggest scratches out then work up to a final fine polish grade as the final step. Boating & RV supply stores commonly carry them, plus you can find them in the larger Jeep catalogs. That's how I would go, both brands work well for this. They require some elbow grease but the results are worth it. And like was mentioned above, one way to keep scratches out is to never ever (!) use paper towels on them.
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When I first got my jeep the windows were in rough shape. I went to a marine store. They guy there game me something for boat tops. It worked great. That was over a year ago and they are still in great shape. Might want to check out a local marine store. Just a thought.
I bought my TJ last week and tried a plastic polishing product from Mothers that I found at Pep Boys. The windows do not look new by any means, but it made a huge difference. It didn't remove any "deep" scratches, but did take care of alot of the cloudiness. I still may try something else to go a little deeper but I am pleased considering I only spent about 20mins on it.