I have done a few of these but on electric basses so the neck to body relationship had different considerations. You may have to release yourself from the idea that the 12th fret must meet the body at one string or another. No matter what, it will cross the body and that will have to do.
There are many variables at play. For instance, if you start with your nut at 90 degrees to the center line of the guitar you will have a very different answer than if you have chosen the 7th fret to be at 90. The fan angles will change making for all kinds of mathematical fun. Without more info I can't comment on your specific issues but here is some basic stuff.
If you use the center line of the neck as your foundation instead of the bass or treble sides it makes things simpler to discuss. Your average scale length is 650 which is the same as the distance from nut to center of saddle between the third and fourth strings (ignore compensation for the moment). In a standard configuration the nut and saddle are parallel to this line. Now imagine a pivot point at the center of each. Leave the nut at 90 degrees and increase the bass scale by 10mm and the treble decreases the same. Draw in the 7th fret (arbitrary choice) and "lock" it to the two outer strings. Move it to 90 and the nut on the bass side moves away from the body and the treble does the opposite.
If your neck is already cut to 650 scale then you are limited as to how you can move the nut end. You can not make it longer unless you go buy that expensive board stretcher you can't afford.
If you choose any fret other than the nut to be at 90 degrees the pivot point that was on the center of the nut will need to move towards the body. This will change where the 12th meets the body as well as the center of the saddle as well as the angle of the saddle. In short I would lay out the bridge location and my nut location and let the fret meet the body as it will.
Fun stuff.
Sorry about being so vague but I don't know enough about your particular instrument to be more specific.
Greg N
) and you don't have to have any frets perpendicular to the centre line of the fingerboard if you don't want to and where/how they cross the body join is up to you.