You may have some structural integrity problems, depending upon how much of roof you plan on removing.
Here are some photos of what the Crossfire looks like under its skin. Unfortunately none are directly looking down at the top.
https://www.crossfireforum.org/galle...hp/photo/17232
From what I can tell, it looks as though there is a sizeable area that could be replaced with some "safety glass" but it goes without saying you would lose the roofs "spine". But since it's only cosmetic and really doesn't extend into the hatch area it would probably look OK.
Getting a piece of Glass made to fit the contour of the Crossfires roof may be a little cost prohibitive, but maybe plexiglass could be used to keep the cost down. Using a dark tinted mylar coating to cover the sections of the roof not removed, and matching it to the tint of the new glass, and the glass in the hatch, might give the illusion of the Mustangs custom look.
Sounds like an interesting project.
I know the place that built my hood could do it, they are fantastic fabricators.
Sounds like a good winter project.
I just noticed that you live Florida (no winter).