This is the way I would do it. First check the string hight with the capo business card trick to see if the trussrod needs to be adjusted or not. Then do the intonation. Then fine tune with the saddle hight.
If the guitar is really out of wack, then you might have to change the order between trussrod and intonation and go back and forth between the 2 since adjusting the truss rod is going to change th intonation.
You follow the radius of the neck for adjusting string hight. All this is coverd by UGB in the tech forum.
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