I've been doing this for two summers without any difficulty. I have gotten some buffeting on occasion but that can happen with the hard top. The sail panels haven't blown out yet even at speeds of 70-75. The one thing I don't do though is run with the rear windows in with the top in the sunrider position. That is not recommended in the owner's manual and I don't take any chances with it. At the very least, I take the rear window out so that no pressure builds in the rear area.
Participate in life....Keep movin'....Go there....JK'n it.........Do it! Jeep #1: Red Rock 08 JK Rubicon 4dr, 6 sp manual, Stock Mud Tires, MyGIG Upgrade, Hard Top, after sale BestTop SunRider Soft Top, Congo Cage Rack, Mopar slush mats Jeep #2 Black 08 JK Rubicon 2dr, 6 sp manual, both tops, some chrome...uggg (my wife's jeep) Jeep #3 White 92 YJ (my son's jeep) A great quote from a good friend: "All hail click clack and master jk'n." Click and clack are my idols!
If you are asking about running at highway speeds with the side windows out and the rear window in, it is not a good idea. First it puts a lot of pressure against your rear window causing stretching and tension on the zipper and second, it creates a lot of drag which can reduce your mpg.
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You'll get bugs in your teeth and your hair will get mussed.
No, you'll be fine.
The Sunrider caution is to avoid the back of the Jeep filling with a lot more air than it can get rid of. Think of air as a fluid, like water - if you fill a container up really quickly, it's got to go somewhere. On a sunrider, if you scoop in all that air, it can blow out the back curtains.
But if you remove all the windows, the air just flows right back out.
Worse case scenario is that the air will push the back bow down a bit (no biggie) and that will cause the back corners to pop loose (again, as InfernoGirl points out, not a big deal).