Even under ideal conditions epoxy continues to get stronger over a period of weeks. Heat treating or baking the epoxy can speed this up, but if your aren't used to doing it on a production basis you're probably better off just letting time and nature take their course.

If the pieces won't come apart then the epoxy is doing its job. If the excess is rubbery or soft after a few days, don't worry. Wait a week or two to see if the material gets stiffer. While you are waiting you can assemble the boat.

I like the idea of reinforcing the scarfed areas, but I don't think you need something as obvious as a block of wood. One kayak kit maker uses unscarfed (butt) joints which are sandwiched between layers of fiberglass cloth. Seems to work fine for them.

You can duplicate this by laying a scrap of fiberglass cloth, 6 to 10 inches wide, over the area of each scarf as a reinforcement. You can do this after the boat is assembled and before fiberglassing the entire boat. Do both sides if you want, or just do the inside. No great advantage to doing both sides as you'll be covering the outside with glass cloth anyhow.

A single coat of epoxy resin is all that is needed on this patch. Once that hardens, sand down the edges of the patch so they form a 1" to 2" wide feather edge which blends into the wood. When you lay your glass on top of this you will have two layers of glass cloth holding the wood together, and the are should be jsut as transpaprent as anyplce else, making the seam and patch unnoticeable.

I think you need some local application of heat in your work area when you are working with epoxy again. A few 100 watt light bulbs put out a lot of heat. You can trap some of that as heated air by covering your work loosely with a cheap polyethylene tarp or drp cloth, and put the lights underneath. the radiant heat will also affect things, so keep the bulbs at least 2 feet away from your work or the tarp. Laying some wood scraps on the floor and stapling the edges of the tarp to them can keep the covering in place. As I recall, 150 watts puts out 512 BTU, so 300 watts would be about 1000 BTU, and should be enough to heat an area the size of a kayak.

hope this helps

PGJ