Sorry.  I meant to say I'd "been unable to find an answer to this question."

   Im building this boat right now, and put the bulkheads together a while back.  I did it by the book and didn't have any problems with epoxy on the threads.  Recently, I've been completing the epoxy fill coats on the interior.  When applying epoxy to the bulkheads, I was a bit sloppy and got some unthickened epoxy on the exposed threads.  I just let it harden, and then screwed the knobs onto and then off the threads, which cleaned off any epoxy.

Sean.

While I built the one-piece EP instead of the nesting version, I can say that after careful consideration, I did deviate from the verbatim instructions in the manual several times to fit processes that made more sense to me to accomplish the same end result or take advantage of tools, products, etc. that I had readily available.  I also found in at least one case where the manual contradicted itself and following the manual instead of my intuition actually made the process more difficult (e.g. adding the transom stiffeners after the boat was assembled instead of prior to stitching the boat together).  

What I'm trying to say is that if you've thought it through and you think your method at worst is just as good as the one in the manual, then there's no reason to not go for it. 

I know that CLC spends a lot of time, energy, effort, and money on their documentation.  They've got some of the best documentation that I've ever seen.  One of the downsides to publishing a paper manual is that it's more difficult to make updates than say a set of instructions that are online.  Plus, at some point you have to consider the manual "done" and move on to the next project.

I would also consider just wrapping the threads with masking tape instead of bothering with wax.  The key is to get the recess completely filled with thickened epoxy.  This location is one of the most highly stessed on the entire boat, so needs to be as structural as possible.

   Thanks for your responses, Sean Mc and Capt. Skully.  For anyone interested, here's what I've decided to do.  I've been troubled by the fact that there is a lot of stress on this area, as Capt. Skully points out, and it seemed to me that there was an opportunity for a lot of lateral movement given that the 5/16" bolts are in 3/8" holes and directionally stabilized only by the epoxy around the bolt heads, at least as far as I can ascertain from the manual.  I'm sure that hundreds of EP's built according to the manual are out there performing just fine, but I've elected to try a modification that I hope won't be much more work than the manual's method but neater and more secure.  That suits my mildly compulsive personality much better.

So, I'm refilling and then redrilling the holes in a drill press with the whole sandwich wired and clamped in alignment.  I'll end up with holes in the aft bulkhead that are 5/16" and holes in the forward bulkhead that are drilled and tapped for the 5/16" bolts.  (I've used this technique in a number of applications on my Pearson 27).  That will provide solid support for the upper 5/8" to 3/4" or so of the bolt with no lateral wiggle room.  As the bolt is screwed into the tapped epoxy, it should not only be secure and captured, but it should also provide a good seal so that there is little or no leakage of epoxy into the interior of the bulkhead sandwich.  Finally, it should be clean because I won't inject thickened epoxy into the counterbore until the bolt head is threaded down to an inch or so above the plywood.  As the bolt is screwed in I can add epoxy pretty precisely as needed with a syringe while the plywood surface around the counterbore is protected by masking tape. 

If the holes aren't perfectly aligned and reassembly of the sandwich is at all difficult, I can still enlarge one or more of the holes in the aft bulkhead as necessary, but the upper half of the bolt will remain captive and stable, which should also make it less vulerable to movement if it's bumped when the hull sections are separated. 

I'm probably overthinking some of this, but I'm excited to try it.