I know options abound for carrying around your side windows and rear window for the soft top when the top is down, but I thought I'd offer up one that works very well.
Start with this bag from Academy (you might have a local Academy store, if not, you can mail order):
Magellan Outdoors™ Large Stuff Bag | Academy
Then add 2 yards of felt from a fabric store, you cut it into three pieces, one large enough to be 3" or so bigger around the edges than each of your windows.
Stack the windows like: rear window, felt, side window, felt, side window, felt
Line up the side windows rigid edge along one side, that's where you'll start to roll it.
Roll it all up and the windows and felt sandwich fits in the stuff bag.
You're on your own what to do about the tailgate bar.