It's the length of the vibrating string, so the fingerboard edge of the nut to the forward edge of the top/high E saddle. The T-O-M bridge is slanted, so only the high E string will be at the scale length (and after being intonated it may sit very slightly back from the nominal scale length by a very small amount, between 0-1mm). So measure from the high E slot to the high E saddle, as that's where the string will run from/to. The saddle can obviously be moved, but you'd want the high E set somewhere near the front of the bridge, as the other saddles will normally be set further back than this when intonated.

The slanted bridge helps with the small saddle adjustment range of the original ABR-1 style Tune-O-Matic bridge (which the AG-1 kit comes with a copy of). The later Nashville style T-O-M bridge has a couple of extra mm of saddle travel. If, when it's built, you do struggle with intonation, then swapping to a Nashville bridge is an option (though I've never had an issue with intonating an ABR-1 style bridge).