For scale measurement u need to measure the lower end of the nut to top of the saddle on High E side and not middle Of the bridge. Since its a TOM there will be a 3degree angle to base side
2. The glue will sit between the curve of neck and body. Need not do anything for it
3. The neck need not line up with cavity. It has to be fixed according to scale Length. If u need to bring the neck further down and if the heel is hitching against the Puck up cavity ( which is never the case most of the times), then let us know. We can let u know what is needed to be done
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