So I spent the extra money and installed a fender mount condenser.
But that is because I treat my M1123 like it's made of Legos. I switch between 2 man pickup, 2 man troop carrier, 4 man helmet hardtop (tall version), and most recently it's been a 2 man with BEOD (Body, Explosive Ordnance Disposal) and the "camouflage net rack" above the cab. No real way to mount the condenser, so I had to go with fender mount, and so far it's worked out great.
Here is my thread about it:
So I just got in a fender mounted A/C condenser to install in the left rear fender. There are a couple things that I need some assistance with. Does anyone know the dimensions for the bracket to hold up the rear of the condenser? I suppose I can just do some measurements of the condenser...
www.steelsoldiers.com
What you might consider is mounting it along one of the fenders instead of across the center. This link is for a guy that did that, mounted on the driver's side fender to keep it out of the way. You lose the fender space, but keep the rest of the bed and the rear visibility.
I was able to find a complete NOS Red Dot A/C HMMWV kit for the M998 soft top or slant back configuration located on the east coast. This is
drivetribe.com
Other than that, you could probably make up brackets to mount it above the 4 man top. It might make the truck look a little odd like that, but it would be out of your line of sight and only lose minimal bed space from the mounting/support brackets.
You mentioned not wanting to lose your rear window. With the red dot evaporator, there isn't a huge choice about that, it's pretty well going to block your rear window (at least half of it) no matter what you do. Unless you go to a different style of evaporator that's just where it was designed to go.