All the issues that Reza and Crunch said are important. Look down the neck and see if the high E maintains the same distance the length of the neck. It's real easy to tell if it's off on your highE or low E cuz you can use the fretboard edge as your straight line. If that's the case, it's an easy fix. Also, Make sure that some bozo didn't put an R2 nut on a guitar that needs an R3, or vice versa. Finally, some guitars neck widths just don't harmonize with the Floyd nut and tremelo systems width. It's one of the main reason I had to stop playing my Ernie ball/MM EVH guitar. The high E on that guitar rides very close to the fretboard edge. Causes you to sometimes slip off the deck when playing up on the higher frets. I compared it to other guitars and it's a couple microns closer to the edge, but it makes for a frustrating experience. Everything else is lined up perfectly on it, but the neck is just a hair too thin in its width in my opinion.