I don't know if a lot of you pay to have this done but I took a shot at mine (because it was so out) on my custom. It come out fantastic. Not sure is this is the formal rout but I'll use the low E and A for example to set the low E string.... 1) Tune the E and the A in basic standard tuning. 2) Check the tuning again at the 17th fret on the E string (High A) .. if it's out adjust the intonation on the for the low E string a bit. (higher or lower depends on your situation.) 3) This will slightly knock out your base tuning so go back to step 1 then repeat 1 and 2. 4) Eventually you will get the high A on the E to match the A string. 5) When you are finished the standard tuning should be correct at the 5th fret (A ...as in standard tuning) and at the 17th fret (the high A) on the E string. 6) Repeat for the rest of the strings. What ever is right or wrong this worked like a charm for me. Happy "intonation'ing"