We installed the four CVI W2 windows on the box this afternoon. We decided that to do the best job we would remove each side of the box so that the lens mounts could be put in place on a flat surface.
The sealant that we used was RTV108 which had very little smell as we were applying it. As you can see from picture 2, it went on pretty smoothly and I'm confident that all windows are sealed nicely. After leaving it to set for ~30mins the windows were installed and the box put back together round the cavity mirrors.
Unfortunately our best efforts at not moving anything have still resulted in the cavity becoming mis-aligned. It is probably as a result of un-dog-clamping the box from the table and then re-clamping it again. Working on realignment right now.