As the thread title says.
When I do the 12th fret harmonic thing, when I fret the 12th fret the e,B,G and D strings are all sharper than the harmonic.

Is this a problem with the bridge or the neck? Cos I'd hate to intonate to have it then like...screw up or something.
Most likely on the bridge, if you have a TOM or a strat style bridge it's fairly easy to do, it's just harder to do on a Floyd.
Jackson RR3 with EMGs!
B.C. Rich KKV
Yamaha F-310 Acoustic

Digitech Bad Monkey.

Peavey Valveking 112
...bridge. You can't screw it up anything by intonating btw.

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