Re: Perfect intonation... HIGHER FRETS ARE FLAT!!!
I seriously doubt your fret spacing is off. I'd try intonating your strings to the 24th fret.
PERFECT intonation on every fret isn't possible. You can get it close, but there is no way to get every note on every string to be in PERFECT pitch. That's why they call guitars a "compensated" tuning system. You have to compensate for variations.
A wide number of variables can affect how accurate your intonation is, including string thickness, fret wear, string height, bridge angle, finger pressure, etc. You're going to just have to try intonating your strings in a way that better compensates for that adjustment.