David~
Just a few quick thoughts:
1) W.E.S.T. is good stuff but very pricey. I buy all my 'glassing materials on-line - resins, fillers, fabrics, foams, etc - from US Composites. I have used their products for several years on boats and decoys and have been very satisfied. Prices are half or less.
2) Re existing coamings and see if you can flex the decks upward at all. New knees and maybe a forward bulkhead - cut from half-inch plywood - might be able to restore a bit of crown to the decks to shed water. Even an inch of crown is much better than no (or negative) crown.
3) Take it slow on replacing the floorboard - but always with an eye toward making installation of a new one easier. Lay out your cut lines very carefully - perfect rectangles or whatever makes sense. I might do some exploratory surgery and cut a hole in the middle of the area so that you can see how it has been built and then inform how you might want to repair or replace. I would mark out a nice regular shape on the centerline (or surrounding a known soft spot) - perhaps 12' x 24" - then cut to the line with a circular saw set to shallow depth.
Further discussions can follow. For example, you could decide to replace the existing floorboard with a removable one.
4) Regarding materials, most new fibreglass boats use no wood for structure. Experience has shown that moisture penetrates the polyester resin used in 'glass layups and ultimately saturates any wood. On the other hand, some of the modern plastic boards (Star Board, for example) are also very expensive. So, you will need to make decisions about how far you want to go. Good fir plywood sealed with epoxy can last a long time.
5) Sketch your vision for the finished vessel. It can be rough but drawing it to scale is best - so you will know what can work and what cannot. It is also helpful to know every feature you might want to add so that you can build in a sequence that makes the most sense.
Hope this helps!
SJS