Just got done doing the same thing, although my windshield is a CMC mounted to a CMC body....I removed it to install the dash trim and just put it back late yesterday.
Look up the CMC/Fiberfab assembly instructions in the "Library" section on this site - not a lot there, but better than nothing.
Once you have the bottom rubber gasket mounted on the glass, then it should line up (more-or-less) with the metal trim piece mounted to the cowl. If you've not yet mounted the metal trim piece, then the CMC assembly instructions tell you how, but I would mount the top frame on the windshield and slide everything into the side mounting posts and THEN scribe the line where the metal trim should fit. Make sure that the windshield is sitting "flat", meaning that it doesn't rock forward to back and simply sits there without the center prop (although you will get a small amount of rocking, maybe an inch at the top).
Now for the bottom gasket. I have a CMC version, and it has a lip on the front that purportedly slips over the lip of the metal trim piece mounted to the cowl. The angle for that lip is totally wrong, at least on mine, so we just pushed the gasket up against the metal piece from behind, and glued it in place with black silicon caulk. Alan's stuff probably works better, but will be harder to get the windshield out if you ever need to, and the silicon stuff has lasted now for 5+ years (it's pretty tough).
As for the Center rod, it should be just about finger tight, no more. DO NOT CRANK THE CENTER ROD DOWN TIGHT!! In fact, the entire windshield should just about float in the frame with very little tension on it, otherwise it will surely crack. It is designed to sit at the proper angle when it is installed on the car, and will do so without the prop rod, BUT it needs the rod for additional center strength. I got the rod nicely finger tight, then one more turn with a wrench - that's it.
Hold everything securely by using silicon caulk (the black, driveway-sealing type) and seal up any pesky gaps around the rubber with it, too (be neat, or it'll make the gasket material shiny).
Good luck. gn