The neck never sits straight with respect to the body. It always sits on a slight angle. There is a slight downward slope at the pocket So a single clamp at the cavity will definitely lift the neck up... I think the clamp has to be compressing the lower part of the neck with the back of the neck pocket like this
As for scale length... Inside of nut to pick up end of saddle with saddle at 75% in bridge in High E should be the measure of scale. Bass sides are always a bit longer to compensate for thickness of the strings. People do measure nut to 12th and double up. But that could be off on the bass side
A wise man once said measure thrice and fix once. Pls do not be in a hurry. Pls do a full mock build and check everything including alignment and angles and pickup pole positions and then take a call.
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