I can't say from your photos whether the deck has been fiberglassed or not. If well done, you might not be able to see the 'glass until you sand into the fibers.
I also can't tell if any of the wood is rotted or not. I am not sure you would be able to tell whether epoxy was applied to the deck before varnishing or the hull before painting. I think it is unlikely that no epoxy was applied to the wood before varnishing and painting but it is quite possible the deck wasn't fiberglassed. I assume that there is a full coat of fiberglass on the hull exterior. You can see an exterior fiberglass seam tape.
First step is to strip all the paint from the hull. I too have had pretty good luck with Citrus Stripper. I would sand the areas of the deck that need sanding. If there are areas of the deck that look pretty decent I am not sure you need to sand down to bare wood. Any areas in which the wood is greyed need to be taken down to fresh wood, and flaking or cracked varnish needs to go, but smooth varnish can just be sanded with something like 120-150 grit paper before revarnishing, unless the varnish is badly discolored.
There is little merit to applying several coats of epoxy before varnishing. You want to thoroughly seal any dry wood with epoxy but several coats will add weight (and expense) with little or no gain in strength. If you want a stronger boat or a better protected wood deck and you find that the deck was not 'glassed, you might consider covering the deck with 4 oz/yd fiberglass which will be completely invisible once the 'glass weave is fully filled with epoxy if it is done right. This will add a bit of weight, but considerable strength.
After stripping paint from the hull, there may be areas in which the fiberglass needs to be patched. I would use 6 oz/yd fiberglass for this and S 'glass is somewhat preferable to E 'glass. You will want to feather the edges of the patches well so that they don't show too much after repainting the hull. To get a really smooth surface before repainting you can fair the hull using epoxy with a fairing compound mixed in such as West System 410 Microlight fairing filler. This is stirred into the epoxy and will thicken it some but is easy to sand down and achieve a smooth surface.
Any surface irregularity tends to be readily noticed after painting so if you want a nice result, spend a good bit of time fairing the hull and sanding it smooth. I would wet sand it starting with something like 180 grit paper and going down to around 800 grit in steps (180, 220, 320, 400, 600, 800) using a soft sanding block. I usually use a disposable sanding block made by 3M for that purpose. I don't use the abrasive surface of the block, just wrap the paper around it.
If you really want a nice looking boat, you might try applying an interior seam tape and sanding off the exterior seam which is pretty noticeable. Applying an interior seam tape is a PITA job though because you have to work through the cockpit opening and the Queen Charlotte has low decks. You can make an epoxy dispenser by mounting a dental syringe on the end of a 1 x 2" furring strip and screwing several screw eyes down the length of the strip. A length of wood dowel goes through the screw eyes and you use it to depress the syringe plunger to dispense epoxy where your arms can't reach. You then smooth out the epoxy with a plastic squeege fit into a notch cut in another stick.
As for epoxy I have used MAS, System 3 and West Systems. All work but I do have at least a slight preference for West Systems. I have found Interlux Brightside marine polyurethane paints pretty easy to use. Apply with a foam roller and tip out with a disposable foam brush. You will need 2 to 3 coats of paint.
The rule for varnish is at least 3 coats up to 7 (or more). I like Z-Spar varnishes (either Flagship or Captain's Varnish) and use disposable foam brushes to apply, wet sanding with 1500 grit paper between coats.
A good source for cloth and epoxy is Sweet Composites or Jamestown Distributors.
Paddler's Truck Rack
Pull-Up Strap Handle Kit
Kayak Motor Kit
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