Squier Standard Telecaster

[marnold***]

Do you think the nut being cut too high on the low E string is also the culprit for the saddle having to be moved so much? Also, I have never had to file down a nut. Is there any way to know exactly how much it needs to be filed down, or would I be better off taking it to a luthier? That in its self could be a problem because there are not may "real" luthiers where I live.

The height of the string probably does have some effect on the intonation at the 12th fret, but probably not much. FWIW, the spring behind the saddle on my Fender on the low E string is about as compressed as it can be, while the others aren't that close.

By filing it down, I mean the slot that the string runs through, not the entire nut. If it's a plastic nut (which I'm sure it is) running that big ol' E string back and forth through it should do it. Just do it a little bit, tune it up again, check it, lather, rinse, repeat. It's much easier to bring the slot down a little lower than it is to try to build it back up again.

[Bloozcat]

The nut slot may also be incorrectly cut in that the break point of the string over the nut may be back away from the face of the nut (bridge side). If thats the case, you could run out of travel on the saddle adjustment before you get the intonation right.