I had an inflatable boot on my Ranger. It was installed (for free!) by the company that sold me the shell and carpet kit after I complained about the increased noise with the shell. The boot stuck to the windows and surrounded the openings of the sliding windows on the shell and carpet kit. I assume you can probably still get such a boot from a company that sells truck accessories like shells and sliding windows.
With my setup the pickup's rear sliding window and the shell's front sliding window remained in place so most of the time both were closed and locked. When I went camping I would unlock the sliders and open the windows for access. I'm not a small guy (6'1", about 195lbs) but I was able to squeeze through the opening without too much difficulty.