Hey,
I'm having the same type of dilema. I'm making a Rhoads V, not a neck through though. I have the two body halves cut out and was thinking of something like this as far as a clamping surface.
Lay out a 2X4 or whatever at a right angle to the center line and mark two lines on the 2X4 where the body ends giving a board that would look something like this:
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| / \ |
| / \ |
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Then I would just cut along the lines and use the 2 outer pieces for clamping. Either that or if the two oustide edges of the body were close to the same angle from center (which I they should be), you could just make one mark and then flip the other piece over and the angles shoule work out to give you something like this:
||
||
/ \
__/ \__
|_/ \_|
/ \
I know the drawings are kinda really shitty but you get the idea.