I've never done it but any chance you could lower the shell down on the frame and get it square and then mark the holes, or drill it in place. Just curious why fiberglass instead of aluminum.
Aluminum is nice, but it's not a bolt-on-and-it'll-last-forever thing. Aluminum DOES corrode, when it comes in contact with salt, or dissimilar metals. There are A LOT of dissimilar metals that come in contact with a tub, including all the bolts.
When I worked at a sheetmetal shop, whenever we "skinned" steel locker frames with aluminum panels, the frames all got primed, and painted,then, there was an electrical tape barrier taped between the frame and aluminum, before riveting the skins on.
It requires a different approach in regard to painting, but, no biggie there.
If you ever get a dent, or it tears, who's gonna fix it?
And, aluminum body parts are more expensive than good quality fiberglass body parts.
These are things to be considered before investing in aluminum.