Sounds like you had several things hit you at once! I think you have all the right ideas for fixing the problem, i.e. joints too tight, too hot, stressed area, etc. If you mix up a thickened batch like Chip suggested you will do much better. Sometimes you may need to coat the surfaces with unthickened epoxy right before joining too. This is especially true on end grain. In such cases, the wood can "suck" the resin right out of the wood flour leaving you with a gritty mixture in the joint. Priming helps stop this. Most of the epoxy lit that I've seen also implies that the faster the epoxy cures, the weaker its bond will be.

The other big area you mentioned is the tight twist at the scraf joint. Try to plan your scarfs so they are not in these regions. They shouldn't line up "around" the boat either, but should be staggered. Since you have this one cut already, consider sistering that joint. If the others are weak, sister them too. Better to be sure than break! Looks aren't everything :-) Because this joint is being stressed considerably, I wouldn't recommend any screws in the sister. They could further weaken the wood. Just use a long sister strip.

When are we going to get to see some pics of this "embryo"?