I use the big washers to keep the bolts from digging into the bulkheads when connecting the sections. So I kept them unattached during construction and only use them on the finished sections.

It's a good idea to coat the edges of the bulkheads with epoxy even before attaching them, but as long as they end up being totally encased by epoxy, you will be fine. Just make sure that you do a good job of sealing them during assembly. I think you'll be using plenty of "peanut butter" epoxy fillets on the insside. After cutting the hull into sections, you'll be sealing raw wood between sections anyway.

   Thank you!

One more question -- I managed to snap off my drill bit in the bulkhead doing the 1/16 holes for the wires.  Grabbed the other end with pliers and it snapped on that side too, so the stub is now fully within the doubled wood of the bulkhead? Should I just leave it embedded and drill another hole behind it? Or try to use a nail or drill to get it out?

I have plenty of permanently entombed wire in my Northeaster Dory. The bit of metal should not cause any problems at all as long as you can completely seal it inside. Jagged edges might slice your hands or feet or something else of value.