Hi Scott, You are right in that the neck measured 323mm from nut to 12th fret crown therefore it should be closer to 646mm at high E saddle not 651mm and will revisit things earlier tomorrow evening after work.

Took some close up shots with a steel ruler along the side of the neck to show the measurements and posted them above for you to have a look at and add your comments.

Beginning to wonder whether nut was cut in about 1mm too far north, ie. towards the headstock and if that might be the main reason things sound out of whack?