I am not an expert but have dabbled in small boat building over the years. If it was my boat I would go for a foam sandwich grp decks and superstructure.
The biggest problem with retro fitting grp decks is that usually you end up laying the grp over a male mould so the rough finish ends up outside .This can be sanded and filled to get a good finish but dont underestimate the job.Depending on the size but even a 30 foot deck could involve weeks of hard work.
If at all possible design and build a female mould.The extra time and materials spent at the mould making stage will be more than compensated later.
Also bear in mind that sanding or grinding grp produces dust which is seriously harmfull to health.
Dont be put off by all this ,a well constructed grp deck and superstructure is likely to be much better than timber and marineply. Totally waterproof rotproof and with good insulation qualities.
A couple of things to consider, have you done an estimate of the cost to re build the wheelhouse and cabin roof plus cockpit floor? And will you be able to recover the outlay when you sell the boat.
Having done that, I would go for the composite structure, easy to build, fast, will not rot, cool in summer, warm in winter and good sound insulation, the list goes on and on.
A bit of long term planning could save you a lot of time and money; do you suspect other areas may fail, if so, you can construct what you have to now but in a manner that it can be relocated / re-fitted later. Also, think about what you are going to attach to the structure and build in areas of fibre based filler to take fixing screws etc. The location and size of openings such as windows, doors, hatches, and vents need careful consideration, you might be able to use existing fittings or be able to pick up some bargain bits.
Some core materials can be curved without cutting slots, just apply plenty of heat; major structural items will need three layers of glass on each side. If you use epoxy resin the finished structure will be stronger and lighter as less resin is required. Epoxy constructions are weaker if too much resin is left in them. Fill and sand to the required finish and paint. Tip, you might find it easier to construct the wheelhouse in sections (off the boat) and assemble when the weather is right.
This is no small task and I wish you and your floating footpath good luck and take care.
You are right about the problem of applying gel coat last over a male GRP construction, however, all is not lost. There are people who are expert at this and, in the same way as you might employ a plasterer to finish off your home-built walls at home, you might be able to find someone to provide a similar service for your boat. Two classes of people who might be able to help are:
1. Surf board builders. All surf boards are built inside out, i.e. no mould. The skill of these guys is fantastic and they might well be able to provide a good final coat for you. They also work with small profit margins and are usually not expensive.
2. Osmosis treatment specialists. Gelcoat is built up on the grit-blasted glass surface in exactly the same way as you need on your new construction.
My experience of building the conventional way, via a female mould, on much smaller jobs than yours, is that it is very time consuming and difficult to visualise the finished job. The cost of materials for a decent sized coach roof would be far higher than bringing in a "finisher" for a day.
Have you considered building the superstructure out of marine ply, then sheething it with woven glass and epoxy resin, both sides, this would be a cheaper and easier way of doing thiongs and you could do a lot yourself, getting somebody in to sheeth it for you, it's just an idea, but to be honest is the way I would go.