I wouldn't have thought that would cause an INCH of misalignment. perhaps a 1/16 or 1/8, but then again I am not sure as I 've never actually seen this happen in person to measure what kind of gap it would create.
that's awfully in depth to start digging in, to not be sure. I would attempt to get it in again, using the methods outlines above and in the How-to.. have a friend help. Ensure the inner CV is secure to the tranny, and that the knuckle is slid ALL THE WAY up the strut as far as possible (further than normal)
These first, then start looking in to replacing a boot.
Ray