Neck relief and intonation

Jeff Moore

Intonation is almost entirely about geometry. The only variable difficult to correct is a badly intonated bridge. I began making my own for that reason.
But even the stock bridges aren't usually a big problem.

You can move any bridge back and forth to resolve both E strings, by fretting the 12 fret and using the 12th harmonic and moving the bridge. Move the bridge until both E's (harmonic and fretted) are the same, even if the resulting bridge placement doesn't line up with the mustaches. From there, you can tell if the bridge slots on the remaining 4 strings are accurate using the same method.
There's no such thing as perfect intonation everywhere on the neck! You can only make the best compromises.
Take heart! A "regulated" (tuned) piano is a far greater mess of compromises compared to any guitar. The devil is in the strings. He'll never be completely saved by mere geometry.

The ruler trick and the 12 fret intonation trick aren't perfect, but are the best tools a regular guy has to see the tress and the forest. A great luthier is usually just an expert in instrument compromises, of course this includes how he/she compensates a bridge. Regular guys need quick and easy ways to measure and make some compromises when things aren't working.

Jazzaferri

Always keep in mind the old joke

How long does it take to tune a guitar? Nobody knows, nobody's ever doe it.

Like a piano guitar tuning has to be tempered. My Peterson Strobe tuner has several standard guitar tunings and several sweetening's to boot.

daffyduck

get rid of your zero fret...problem solved