Hi Will, ... what Brendan said ("don't touch the fretboard!") couldn't be more spot on ... even though it might seem like something is amiss with the measurements the overwhelming chance is that they're actually all fine (these kits are pretty damn accurate)
One thing to be aware of is that the tune-o-matic bridge isn't meant to sit square to "string-line"/neck - they're actually at a slight angle (very roughly about 3 degrees out of square) ... so you should have a slightly longer measurement from nut-to-bridge on the low-E (bass) side than on the high-E (treble) side ... so you're measurements are sounding pretty much like they ought to.
... and great choice on model (I love a nice EX - its some serious rock-n-roll stylin') and you're plans for it sound like you'll certainly be doing it justice! Really lookin' forward to seeing this baby come together!
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