Ain't nothin' but a Gear thang, baby!
View post (necks, truss rod, intonation... suck@&$)
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I also agree that you should bring it to a pro until you are comfortable working on it yourself. You might want to find a beat up guitar at a pawn shop to practice on. One thing to keep in mind... you're not going to find an Ibanez that has perfect intonation. The twelfth should be a bit flat or sharp. Just not too much. You were on the right track until you started trying to adjust to all the other frets.