Well I removed the 06 regulator and cut out my support brackets for all of that and re fitted the door with the 2010 Challenger regulator which is designed for a frameless glass application. You can see the vertical runners are spread wider to carry the load more evenly. Also the glass clamps are much bigger. Other features that are built in are the adjustable stops for the glass and the adjustable mounting studs to help angle the window in the opening. Much simpler set up even if it barely fit into the door. I still may have an issue with the upper seal when I close the door as the Challenger uses "Smart Window" technology to bump down and then up when opening and closing the door. Maybe later I will attempt to learn the particulars of that set up but for now I just swapped the 6 pin motor for the 2 pin deal that came out of the 06.
Talked to Lee out in California about the glass today. He has my Lexan window and he sent pictures of it overlaying the glass from the F&F cars and except for having to cut the front edge off to match mine they are a pretty good match. Probably a couple of weeks before I see them.

Well it is time to back out of another dead end I have driven down. While the Lexan side windows look okay there are several problems that can't be overcome. The windows on their own are not strong enough to seal well against the roof/A pillar gasket. Part of that is due to my insistence on using the 06 Charger window regulators. The regulators are meant to just run small windows up and down in a confined frame. Frameless glass needs something a little more robust. I took a look at some 2010 Challenger regulators and they have the same design but with 2 important differences. The clamps that grab the glass are much larger to torque the window over against the seals and the two vertical runners are further apart to accommodate the longer glass (Better weight distribution) So I ordered a couple of those on the Ebay.  I had a talk with Lee at Alan Auto Glass in Burbank Ca. and he assured me that of the 10 cars they put windows in (6 for F & F and 4 for Drive Angry) there were no breakage issues and he is pretty sure they were somewhat rough with those car. So I have decided to go out on a limb and get a set of the side glass he has left over from those two projects.   Either way I don't think I am breaking any news here to say that the roof seal is kind of crappy and I don't think I will ever be happy with that. I guess that is why the new cars have that feature that drops the window a bit when you open the door and then automatically runs it up into the seal when it is closed.  Remind me to start with a Challenger next time. It has all the right bells and whistles for this kind of conversion.

By the way the pictures show a steel "C" channel I had to run around the perimeter of the Lexan to get it to be rigid enough to hold its shape. It didn't look as bad as I thought but it was not what I had in mind.