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However, yes - I check the 1st string and the 6th string and set the truss rod based on the smaller gap of the two.
I never use gauges or a capo, just fret the string with both hands while holding the guitar normally - this is important, if you do it with the guitar lying on its back the relief will appear less than it really is because the weight of the neck will pull it back slightly.
A very slight twist with more relief on the low E side is ideal, in fact - as long as it's even. It can be caused by the reaction to the truss rod nut being tightened against the washer, if the adjuster is at the head end. With this one I would loosen the rod just enough to get perceptible relief on the high E and see what happens to the low one.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
Bad news....it looks like my guitar has a twisted neck.
Good news....I still might be able to set it up so as to play half decently.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
The thicker strings need more relief than the thinner strings. The high E usually needs no relief at all, so your neck fits that perfectly from the sounds of it.
In practice it means you get lower mid-fretboard action on the thinner strings for the same 12th fret action than if your neck had the same relief across the strings.