X2 on Plexus if your windows are in good condition to begin with. Plexus is such a mild polish that it won't remove any scratches but it does do a really good job otherwise.
Lemon Pledge doesn't remove scratches either, it only temporarily fills them with wax to temporarily make them look better. Being as it only uses wax to fill minor surface scratches, it doesn't work very long.
If your windows are scratched up from having used paper towels to clean them, then a multi-step plastic window polish like from Novus or Meguiars will be needed. Plastic window polishes can be found in boating and aircraft supply stores since they use plastic windows, you won't find it in automotive stores.
Finally, never EVER use paper towels on the Wrangler's soft top windows. NEVER. Paper towels are made from pulverized wood products and their use will absolutely 100% guaranteed eventually put a haze on your plastic windows which will eventually cause them to turn opaque and yellow. To clean them, rinse them off first and then after gentily wiping them with a mild soapy solution and soft cotton cloth, rinse and then dry them with an old soft cotton towel or tshirt. And never wipe them when they are dirty... vinyl windows are so soft that they are very easily scratched from wiping them when they are dirty.