It seems like (and is) a big job right now, but this is probably one of the most important junctures of your boat. The bulkhead is that thick because it is responsible for transmitting the stress of the rig and distributing it to other parts of the boat.
I think that filling it with epoxy is a really dangerous idea. In the end, you are liable to end up with an even weaker boat. The bond formed between old, deteriorated wood and the epoxy will not be strong enough to deal with the load.
You might be able to cut away the rotted part, replace it with new, well-sealed wood, and then sandwich that between two EQUALLY STRONG pieces of wood that are through-bolted (lots of bolts here - not one or two) holding all three pieces together. Make sure that the pieces on either side are much larger than the one in the middle, and make sure there a lot of bolts on the perimeter, as it is these bolts that are taking and distributing the load - not the sandwiched piece in the middle.
Good luck and let us know what happens...
The sooner you deal with it - the better.
Last edited by Sailormann; 04-22-2007 at 12:06 PM.