Ah, the zero fret. Yes, scale length is from the middle of the zero fret, not the nut in this instance.
It's only going to be a couple of mm out, and slightly further back than it should probably be (though it looks quite forward compared to the original bridge holes). So it's probably time to fit all the tuners, bolt the neck on and string it up. You should be able to hear enough acoustically to determine whether you can set the intonation correctly (using a tuner app on your phone should help). You may find that you're fine. If not, you'll know for sure and can then plug and drill (again) before you apply any finish.
Last edited by Simon Barden; 09-08-2018 at 08:21 PM.