If it's vinyl, I would get the Ragg Top Vinyl Convertible top kit. I just got it and it's great. I used to use 303 on my convertible top, but I didn't think it bonded well with the vinyl.
I was going to suggest the Ragg Topp product but Mike beat me to it...They make great stuff for all rag tops....For your plastic window look into Novus for cleaning, clearing up scratches and yellowing. It comes in three different levels one and two will be more than enough for you.
I have a wrangler too. I think I am going to try the rag top stuff. For the windows Mopar actually makes a window cleaner for the soft top. It also gets out light scratches. I tried it on mine and it really seems to work well.