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If spacing of the low-E to the edge of the fretboard is ok then it doesn't sound like the neck. Basically the string spread (distance from high-E to low-E) should be centered in the neck, if it isn't then the neck may be offset. For example, if you were to shift all strings toward the low-E by the same amount, would that solve the problem? if yes, then the neck can be moved slightly (slightly!).
All this is kind of hard to diagnose over the web with no photos, so it may be best if you take it to a guitar tech to get a "hands-on" opinion. I would not want for you to start messing with things based on our "guessing" and create a bigger problem.
Jon
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