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When I put my truss rod into the channel there is .04" gap between the top of it and the top of the neck. Is this fine or should I plan to make a thin insert?

what truss rod do you have?
If it is a martin you lay a bead of glue in the channel set in the rod ad another bead on top and glue that and the fretboard in all together

_________________
John Hall
Blues Creek Guitars Inc
Authorized CF Martin Repair Center
president of Association of Stringed Instrument Artisans
http://www.bluescreekguitars.com

It's actually one of your kits John, so I'm assuming it's Martin, but not sure how to tell.

I went ahead and made a veneer while I was working on other things last night. Are there pros/cons to either approach?

veneer is fine but not needed on the 2 way

_________________
John Hall
Blues Creek Guitars Inc
Authorized CF Martin Repair Center
president of Association of Stringed Instrument Artisans
http://www.bluescreekguitars.com

Is there any reason some of the other instructions say to keep glue away from the truss rod channel? I saw this in other build manuals and wasn't sure why.

I've used glue in my channels and have never had an issue.

Maybe there's another reason, but it could be that you see instructions not to use glue truss rods, to facilitate replacing the them, should something happen down the road. I had to replace 1 of my rods, and all I did was remove the rod, clean the channel, and replace it. It was no big deal.

Don't use CA glue; I could see that possibly causing problems. I just used original titebond.

the older instructions were from the 1 way rods that had open threads. if the rod is sealed in a plastic shrink wrap all the glue is doing as acting like a filler to control rattle.
be careful don't mix building instructions from one kit manufacturer to another.

_________________
John Hall
Blues Creek Guitars Inc
Authorized CF Martin Repair Center
president of Association of Stringed Instrument Artisans
http://www.bluescreekguitars.com