First off, I like David's suggestion. I work well in autocad, visualizing everything on a computer screen (being a mechanical draftsman for 8 years will do that for me). But lay it all out and you will be able to visualize the proceedure better.
There are three trains of thought (well maybe four) for when to level the fretboard, of which option D has been discussed here recently and has some controversy surrounding it
A: Shape and level the board after it is glued onto the neck blank ala Cumpiano & Natelson's book, install the frets, shape the neck (see below for internal wood stress'), finish the neck and body, attach the neck, level the frets (crown & polish). This might be the least common method for people who have built a few guitars. Wood has internal stress' which do funny things to the wood when you remove material. By shaping the neck after the board and frets are on/in, these internal stress' can change the geometry of the board leaving you to leveling again after the neck is shaped.
B: Level the board after it is glued onto the neck blank and the neck is shaped to 95%(+/-), install frets, finish shaping the neck, apply your finish to the neck and body, attach neck to body, level the frets as needed. With the neck blank shaped there should be no released stress' in the neck wood. Now you've installed the frets after the board is level, this can often induce some slight to moderate back bow into the neck assembly which will need to be leveled by either the pull of the strings, plus some action from the truss rod and leveling the frets.
C: Shape and level the board, glue onto the neck blank with the neck shaped to 95%(+/-), finish shaping the neck, apply your finish to the neck and body, attach the neck, level the board one final time than install the frets, level the frets as needed. This may be the most common way of doing the procedure. You get one final time to make sure the board is level before the frets go in. Once the frets are install, there again will most likely be some slight back bow induced by the frets pushing the fret slots apart. Again the frets will need to be leveled by either the pull of the strings, plus some action from the truss rod and leveling the frets. Some folks don't like this way as installing frets over the body can be intimidating.
D: Get the board and neck level before gluing to one another. shape the neck to 95%(+/-), install the frets on the board, ensure the board is dead level (like really dead level, see some of the discussions in the archives on this method), glue onto the neck (with some sort of dead level clamping caul over the board), finish the neck and body, attach the neck to the body, level the frets as needed. This method ensures that there are no internal stress' on any of the pieces. You've removed the majority of the wood from the neck, you've installed the frets and made sure the fretboard is dead level before gluing it onto the neck.
All of these methods will require you to set the neck angle at some point, either before the fretboard is glued on or after, you'll have to decide when, but I would suggest it be set primarily before the board is glued on but after the neck is mostly shaped. Once the board is on and the finish is done, you can check the neck set just before you attach the neck to the body.
The other issue in making your neck is the glue you choose. Many folks use a PVA glue like titebond or LMI white glue. These glues have water in them (although only a bit, water none the less). Water swells wood which can cause it to warp. It is becoming more common practice to glue the fretboard to the neck with epoxy (which doesn't have water in it) to eliminate the possible/probable swelling of the wood.
The controversy behind method "D" is that it's difficult to unsure everything is dead level before you glue the fretboard on to the neck. It's not impossible but difficult and will take some trial and error before getting it right.
You decide the best way to go. I think most would tell you to use option "C". Personally, I'm going to do my darnedest to make option "D" work for me.
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