Because I don't have a 2-door JK, there's one detail I had to write about but couldn't take photos of and that's how the roof panel gets attached to the main hoop of the roll bar for running with the sides off. Obviously you've taken care of that, so if you could post photos and a description of what you did that may help other 2dr owners, and also anything else you've done to support the rear of the roof when the rear panel is out.
To support the roof panel, I used four support points - two in the front, and two in the rear.
In the front, there is a plate that sits on top of the roll hoop structure on either side. I tapped a hole in that plate because it's pretty thick, and just used some 1" aluminum square tubing as a spacer to run a bolt through the roof panel to the plate. I seem to have neglected to take a picture of that spacer, so here's a shoddy picture of the right-side location. You can see the plate that I tapped a hole into:
In the rear, I made brackets out of shaft collars, some 16ga steel and that 1" aluminum square tubing - just what was available at Home Depot. I riveted everything together because I don't have easy access to a welder since moving. I created the shape using some scrap cardboard after I completed the rest of the top. Too lazy to use CAD for such a simple and imprecise part, so I used a copy machine to create the template:
Here's the final right-side bracket, left unpainted until I motivate myself to do so:
With the sides and rear removed, the top really doesn't move much at highway speeds. Without doors and the freedom tops, the roof panel oscillates up and down by maybe 1.5" total, but not enough to worry me. My brackets are as close to the corners as I can get, but they're still not very close. Here's a picture that somewhat shows where the four bolts are located:
I'll come up with a list of points you could add to the instructions, but they were pretty thorough to begin with. Any and all further questions are welcome!
-Harrison