Welcome decibel boy,

If you could post photos it would be a lot easier for us to see what you mean, and I haven't made one of these so I not sure of issues that others may have had with this. (Someone who has made a JR kit might chime in with their scale measurements.) Having said this the distance from 12th fret to bridge will usually end up slightly longer than nut to 12th fret to achieve intonation, 5mm seems a bit much though.