I've never worked on a micro-tilt neck, so take this with a grain of salt.

I assume the measurements you gave are made at the body end of the neck, and that the nut slots are spaced correctly. In that case, you should be able to align the neck by slacking-off the strings and slightly loosening the neck bolts. You can check the alignment by pulling the E strings snug from behind the guitar body. Then tighten the bolts again.

Good luck. Let us know how it turns out.