I had been to the dealership looking for the cleaner for the soft top windows. Their parts department isn't very helpful. They didn't stock anything and they didn't even bother to try and look it up. They don't even have the lube for the zippers so I'm positive they aren't servicing it when I take it in. (Anyone have a good zipper lube option?)
So at Walmart last week I saw Meguires PlastX for clear plastics. I found it worked really well. It removed small scratches and polished everything. Water beads really easy on it. They actually looks better than the glass windows.
It is a blueish colored micropolish. I was concerned at first because after doing it and going driving, the windows had a slight blue tinge but that seems to now be gone.
When I used the rag to do the outside, it turned gray from all the dirt. Inside was almost non existent. If you forget to wipe it off inside, it leaves swirl marks in the condensation,

but isn't visible when the condensation burns off.
Here' the website blurb;
"This easy-to-use, rich gel formula quickly restores optical clarity to both rigid and flexible clear plastics. Cutting-edge advancements in Meguiar’sŪ exclusive Microscopic Diminishing Abrasive™ Technology (MDAT) remove light oxidation, chemical degradation, surface contamination, stains and light surface scratches with ease. Special highly water resistant polymers provide long lasting durable protection to keep your clear plastics clear and beautiful longer."