The way I stored mine in the past is for a TJ and my old YJ only had a hard top and bikini, so this may not help a lot.
I purchased some "soft felt type" material at Walmart and had a window bag made to store ALL the windows in when I had the top dropped/ off. You wouldn't need the full bag with zipper since you are not taking it with you as I was. When I started running a Bikini top, duster and jammer, I stored the windows in the "bag" under the bed in the bedroom.
The frame work and top itself I hung on large L shaped Hooks in the garage.....with a little D-con laying in the folds of the top. It does stick out from the wall about 18"