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I'm about to glue my fretboard on and I've been wondering about the truss rod. I assume that when I adjust the truss rod it braces itself against the bottom of the fretboard to force the neck to bend up or down. That seems to me to be a lot of force. Does the fretboard glue joint actually take all that force. Is it strong enough? It seems to me that it could easily pop off.

There sure are a lot of guitars that are out in the world that shows that it works; the fret board does not pop off. There is a lot of surface area for the glue joint. The force against the joint it is somewhat distributed.

Ya that's true. I just wanted to make sure I wasn't missing something. Should I put a piece of wood over the truss rod channel so it sits flush with the fretboard?

I have placed a strip of wood in the slot and planed it flat to the neck, but only when I was a bit deep. Normally I run a bead of silicon chaulking down the center of the slot to keep it from rattling.

A lot of times it comes down to the design of the rod as to whether it should be capped or not. Most one piece single action rods like Gibson uses need capped, most double action rods do not. That said you of course can always cap one if you choose for whatever reason but I don't think it will have any bearing on function or longevity. I use the SM hotrods with no cap and no problems.

I think it depends on the design of the rod being used. The designs may be similar but there is a big difference between the stew Mac and Martin design. I use the martin style. I have used caulking and just a layer of tite bond to fill the voids. Both seem to work fine.
Personally , if the neck is well built you really don't need the 2 way rod. In 13 years the only necks that I saw that needed forward adjustments were ones on hand quilts that were not done properly. I love stiff necks and use tee bars on some of my guitars with compression fretting.

I use the Martin design and epoxy it into the slot. This gives a very stiff neck and transfers force directly to the neck wood.
Tom

I run a bead of silicone caulk in the bottom of the truss rod trench for rattle prevention.

David L