Hi Retro

Just a couple of things I learnt when finishing my ST recently.

You should measure from the nut to the middle of the 12th fret. Then from the middle of the 12th fret to the bridge thingos (adjusting bits - sorry) should be the same. About the middle. You see the bridge already has been adjusted to somewhere near the expected during intonation. I hardly needed to move mine.
As long as the "same" is within the adjustment you should be fine. A PB expert may be more helpful.

Second, if you are going to use the whammy bar make sure you leave at least one mm between front of the bridge and the pickguard. This ensures the bridge does not bind on the pickguard when using it. This mm will of course be part of your setup measurements.

There is a good articles on the StewMac website. You can find great videos on YouTube. Look up fitting bridge.

Greg