You've got a project alright.
IMO - step one is to decide what net shape you want to end up with. If there's enough headroom without going up farther, then maybe recreating the inner roof contour is your goal. If you want more headroom or skylights, then you have to design that first.
Front to back - how long is the opening?
+1 on System 3 or West System. I've used the latter for a long time, but I think the brand doesn't matter. West also has a technical guide which is very detailed. It's geared towards boatbuilding, but that's essentially what you've got - an upside down boat hull.
If I was recreating the inner roofline I'd do something like this:
Find some structural fiberglass to make up for the missing 2x4s. I'd start with channel or tube sections that best matched the thickness of the core. No harm in having more than what was there originally. I'd start with three anyway. Here's an idea, match the 'leg' height to your core material.
https://www.grainger.com/product/FIBERGRATE-Fiberglass-U-Channel-3-in-4ATN2? If this isn't long enough, there are plenty of other sources. You could even use 2x4s again but I'd want to do something stiffer and inorganic. As in boats, any deck penetration is a potential water leak and core degradation.
Then I'd scoop out at least 3" of core all around. They do this in boat building when fixing cored decks - get back to clean, dry materials.
I'd put the channels in with epoxy. Stuff the ends into the core area front and back, legs down. Maybe right next to the original 2x4s or what ever is there. Add some thickener to make it like smooth peanut butter. They sell this but really fine sawdust works just as well. Butter it thickly - weight doesn't count against you - you're not building an airplane.
Then, from bottom up, take some composite fiberglass sheeting like they use for shower surrounds and build the skin. Sand roughly where gluing. Use temporary springers to hold the shape while gluing. Put fillets on the top where the skin meets the channels with more peanut butter. Glass over with 3" fiberglass tape.
With two or more overlapping layers of skin (build up to approx original thickness), add foam panels to match/replace the core. Stuff the foam into the core areas to tie it together.
Once it's skinned and cored, apply the outer skin same as the inner.
One last thing - epoxy is more expensive, but reliably bonds to more things than polyester. Polyester resins used for automotive use styrene in the catalyst, and that will eat most foam products. If you can paper mache, you can fiberglass.
Use plenty of PPE - long term exposure to the hardener will result in allergies.
