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Uh-oh. The proper method for setting up is truss rod, bridge, then nut. If you get the string slots too low without straightening the neck and lowering the action at the bridge the strings might end up laying on the frets..... And I don't check the action at the 12th anymore because my clients play the whole guitar. I check action at the last fret....

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"Act your age, not your shoe size" - Prince

Now here is where we are going to disagree Chris and no problem whatever works for you or I as they say.

I'm adjust the truss rod, then cut the nut slots and you are not taking them too low because you use the method of fretting and holding between frets 2 and 3 and this takes the rest of the neck out of play.

The benefit is that I can adjust the truss rod, cut the nut slots and now these two things are done and will not have to be changed in the final set-up. Now I do the action at the bridge and of course the saddles need not be changed in a final set-up, in fact there is no final set-up.

Just like computer code doing these three things in sequence rod, nut slots and saddles and there is no back tracking ever each adjustment functions as a function of the prior adjustments and as such they all work together because the three adjustments were all functions of each other's adjustment.

So let's say I don't do the nut slots but do the rod and saddles first. When I cut an ESP or PRS SE nut slots as I just did this morning and then I measure my action at the 12th it went down because I took the nut slots down. Now I have to do the saddles again and raise them.

So the saddles and slots have an inverse relationship much like a teeter totter where what I do with one impacts the other EXCEPT when I cut the nut slots in isolation by fretting and holding between the 2 and 3rd and observing and reacting to what I see.

This single thin, finding a proper sequence to doing a set-up has made us a lot of money and made my life much more enjoyable in that I can really move though the set-up now and there are no mysteries, it all makes perfect sense now that I understand the dependencies here and what is a function of what else.

So again it's truss rod (and there is a lot to say just on the rod because people rarely adjust them correctly...), nut slots cut very low and then saddles.

Next I set action for what I think the instrument if capable of and this takes a LOT of experience to know who uses PLEKs and who uses them well.... not the same thing and who finishes up with hand work knowing as I do that hand work can be superior to a PLEK. BTW Collings is PLEK and finish with hand work which is why I now own two of them and want more:)

I'm going to start a new thread on how to properly adjust a truss rod because I strongly suspect that some just don't know.