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So do I apply glue to the M & T joint as well as the bolts or just bolt it on dry? Also should I glue the heel to the body?

No glue in the motise and tenon joint nor the bolts. Only glue down the fretboard extension.

Alain: No glue on the M&T joint. My own personal guitars that have this joint don't even have the fingerboard extension glued. A couple have been like that for at least ten years with no problems except lost of power in the notes of the frets in the extension. I certainly never use those anyway. If you are going to keep the guitar for yourself you can wait a while to see if the action is going to raise a bit.It may save you some work if you have to reset at an early date.You can always glue at a later date.
Tom

If you have 2 bolts you are fine , if it is a Martin neck ,that has 1 bolt and is designed for glue.

+1 what John said.

So do I glue the heel to the body?

Alain: For a normal two bolt M&T joint the only part glued is the fingerboard extension.
Tom

Thanks