For Soft Top Window storage I just purchased the Jk wrangler 3 compartment bag from Mopar. The part # is: 82210326. You can buy this on E Bay from $69.00 plus to Mopar at $100.00. I have read other posts here and there on the bags and decided to post this.
The bag is of good quality. The inside "blue cloth" is something like a paper but the construction is good too. It even has clips on it to store it when rolled up. One note on this type of bag you take the rear window bar off and store it with the soft top in the boot.
Here are some pics:

 

I too have one of those. Haven't used it yet but plan to when it warms up a bit.

 

Did you get the boot too for the soft top? And if you don't mind how much $?
I'm thinking of getting the boot . The one that comes stock is pretty light weight.

 

I have a neighbor with a tricked out 01 TJ and he uses his Window Roll from Clover Patch all the time and loves it. Then I found out that 4WD Hardware has the 07 Window Roll for both 4 door and 2 door.

I just got mine today from 4WD Hardware and it has thick felt for the quarter and rear windows. You can store the tailgate bar if need be. Do you know that the rear window on the JK has zipper teeth that can and will mark up the rear window. Well, the rear window felt is made to go under the zipper protectiing it. Great thinking. My neighbor has the original 01 windows, they are scratched from tree branches, but are clear as a bell. I guess mine could look like his for $$.

Under $80.00, worth every penny. The windows go in a nylon tube and strap to the roll bars, out of the way. Best part is they are with you.

 

Now you have me thinking? Your (Clover) sounds better engineered.

 

Just wondering if the Mopar storage bag part number is for the unlimited or 2dr version. Will it work for both?

 

This is for a 4 door. I'm not sure of the 2 door number.

 

I just looked at the mopar site and they have the two door version but it is different. It is capable of holding the front upper windows and all rear windows. I hope the 4dr rolled version will work since it sounds like it only holds the rear windows and rolls up so you can set it behind the seats.

 

Yep, my neighbor has grand kids and what he likes with his Window Roll, he straps the Window Roll to his roll bars and they do not take up room. I want to take my windows with me in case it rains or I'm out too long with the wife and it gets too cold for her. Pop them in and I'm good to go.

 

I just returned mine and bought a Clover Patch. Thanks for the help!