OK - Beginner here on B1L5 but I am an engineer and pretty good mechanically.
I watched the guitar setup series of videos here pretty carefully -
https://www.justinguitar.com/modules/set-up-your-electric-guitarI also have a very slightly used, new to me Squier Strat. The (pawn shop) salesman said, "The owner is a guitar wizard and sets up al the guitars..."
The first thing I then noticed is that all my bridge blocks are dead level - hmmm... So I decided to start measuring - down the rabbit hole I go - LOL
The first test is to fret the third fret and look for a "little" space above the first fret - Zero space, string is hard aboard the fret. So, "God hates a coward" as my dad would say so I adjusted the truss rod and got a little space.
Then of course the action down the neck is way high. I worked through it and got the action decent enough. TBH - I have a "cheap" plastic gauge that only has a "low" and "high" setting but have a metal precision one coming so I can't give an accurate number yet.
I set them pretty much at the "low" setting. Then I worked the intonation and as the video suggested it was way off. I don't have a strobe tuner but I do have a really good tuner and now all the strings ring true note both open and 12th fret. And yes the bridge blocks are definitely not parallel to each other any more. Also, for example, no matter what fret or string I play an "E" on the tuner calls it an E. That was definitely not the case before I started.
TBH this whole thing started when practicing the pentatonic first position - certain notes didn't sound quite right. Then when I first checked almost all the 12th fret notes were way sharp.
So much for pawn shop wizard - I can say that the playability and sound is noticeably better even for a newbie like me.
So - finally here is the question. The initial first fret gap is still tiny but the bridge blocks "seem" to be wound quite low (lots of thread sticking up) - I could make the first fret gap a little better (like in the video) but I'd then be winding the bridge blocks down even more.
I did wind the sixth (low E) and A up slightly as I was getting a little buzz up to like the 3rd fret. I figure this is a bit normal on the fatter wound strings to need a little more clearance.
So - is my nut OK and I am doing OK or am I off base in my tuning? It's almost like the whole nut is low a bit but being a "like new" guitar that's not a good explanation.
The only thing I am judging this by is how much allen screw is sticking up from the blocks.