As you have already identified one error in the neck pocket construction;
- You could fit the neck in the pocket and check for correct alignment with strings fitted (but not tight !).
- Also, you may wish to check the scale length is correct with the neck fully home in the pocket
- just to ensure all will go as expected, you could also check that the screws enter the neck vertically. Any error here will have implications for holes in the body
Then,
Once neck is at the desired position in the neck pocket, mark the end of the body on the rear of the neck (a piece of tape carefully applied will give a nice line). Note if there's any discrepancy between the side of the neck and the side of the body, you will have to allow for this later if there is a difference
Using tracing paper (or greaseproof paper does just as well), trace the back of the neck using your tape mark as a reference point. Ensure you mark all sides of the neck as well as the screw holes
Apply decorator's masking tape to the rear side of the body over the neck pocket area. Place the paper to account for any discrepancy found between the side of the neck and body. Then use light pressure to transfer your tracing marks to the masking tape (make sure you don't turn it over !)
Double check everything. Think twice, cut once
Good luck with the project