Hi jarro.
I also use nut files for all my nut action adjustment and have a slightly different approach than Simon but his advice is solid.
Presuming you don't have nut files, I addressed the issue of nut height adjustment by sanding the bottom of the nut in another thread recently, and being lazy, I've just copied & pasted the reply I posted there:

re: the nut, yes, you can adjust it from the bottom. You need to be careful to not sand an angle in the "front to back" direction.
You may wish to put a slight angle on the E to E direction so that the bass E is higher than the treble E.

When you sand, don't do it freehand. Use a block that you know to be flat, placed on a bench/table and put the sandpaper on that working the nut across the sandpaper. A plate of glass makes a good flat surface for doing this, and you can sticky tape the sandpaper so it doesn't slide around too.

When you measure the nut action, you want to depress the string at the 3rd fret and measure the clearance from the bottom of the string and the 1st fret. Since you won't be adjusting each individual string height, just measure the two E strings presuming the nut slots are radiused from the factory. The best way to measure this is with feeler gauges.

As a rough guide, you want the bass E to be .010" - .008" and the treble E .006" - .004" (at 1st fret, string depressed at 3rd).
FWIW, I just measured one of my strats with a 2-point vibrato on it, and the bottom of the bridge plate is 3mm above the body with the fulcrum points and "knife edge" adjusted accordingly. I have the spring tension adjusted so the bridge plate is parallel to the body (I also have a stop shim, but that's not relevant here). My string action is right where I like it - bass E: 1.75mm and treble E: 1.5mm at the 17th fret.

As Simon has pointed out there are a number of ways to gain or lose a couple mil if needed, but I would check all the things he mentioned first and not get too hung up on it in this stage of the build. I don't think it's anything that can't be addressed in the final set up. That's one of the good things about screw-fixed necks, you can always take them off to make adjustments or modifications.