I've epoxied my bulkheads and transom with their doublers. Being a noob, I neglected to clean up the "slag" (epoxy that was squeezed out of the "sandwich) and have been cleaning it up. Reading ahead in the manual I've realized most of this cleanup is unnecessary. In fact it might be better not to since I could damage the wood. I think the only place that needs to be clean and flush are the surfaces that join other surfaces, such as the top (with the thwarts) and bottom edge (joins the floor) . On the other hand, the edges of the doublers do not need the slag removed since they will be covered with fillet. Also, most of this will eventually be covered with flotation and thwarts, apart from the part of the bulkhead that rises above the thwarts, and most of the transom. 

Wanted to log this for posterity, but I do have questions:

1. Is it true that I can just apply the filleting to the slag?

2. Will I ever want to look at the bulkheads without the flotation? Not trying to cut corners but I don't want to spend time making something pretty if it'll be hidden forever.

3. Is now a good time to trace the bulkheads' shape for the flotation, before stitching them to the hull? They don't mention it in the manual. Is there a reason for doing that later?

4. Is now a good time to apply epoxy to the edges of the limber holes, otherwise that will be endgrain exposed to water pretty much anytime I'm out in the boat? Doesn't seem to be mentioned in the manual.