The way I do it is:

Neck relief/truss rod adjustment -checked with notched straight edge.

Check for raised/loose frets and tap them home.

Light level and dress. Marking the frets with texta and using a radius block on ~600grit will give you a good idea if there are any high or low points.

Set action to ~1.5mm at the 12th fret.

Intonation.

Then I play it for a bit, and tweak the action till there's no buzz.

Over the course of a week or so I'll keep rechecking relief as the guitar settles in with string tension on it.

After I'm sure it's holding adjustment I'll do a final set of the action and intonation. It's at this point I will start fine tuning the nut. Quite often on the kits it's too tall. You can file the bottom a bit to bring the overall height down (and sometimes I do this right away if it's ridiculously high) but you do need to lower each slot individually to suit the string. I normally use a feeler gauge and try and get it down to a little less than .5 off a mm off the 1st fret. Like the rest of it, I find it best to creep up on it in small increments.

When I'm happy with the nut, I'll re-check and fine tune the action and intonation again.

Generally speaking, depending on how much I'm playing, it usually takes a bit over a week to get it really spot on on a freshly built guitar. Once it's seasoned I only every really check it again during string changes or if its playing up.