I would hit a shipping store, they have a stiff foam that comes in a roll, comes in various thickness's. That kind of foam would tend to sit flatter between the top and the bars. There was some discussion on this back a few years ago on jeeps+willys newsgroups about the time the sailcloth tops came out and I remember there being some rather ingenious solutions. I did not have a TJ at the time so other than a passing 'sounds good' I did not pay much attention to it.
There is a german company thats makes soft top liners for S2K's, it's discussed here http://www.s2ki.com/forums/index.php?showtopic=497560
Thinking about it I wonder if a bikini could be rigged up under the soft top and the area between stuffed with some kind of insulation, now you have me thinking, usually I just drive my cherokee in really bad and cold weather.