Neither link seems to be correct.
Yes... though, since it feels "a little funny", you may still want to double check it.
It may be difficult for anyone to help without the diagrams or a snapshot of your wiring. The fact that the neck pup is coming out alone in the correct position would indicate that you've oriented it correctly. With even a slightly complex wiring job, it really helps to be EXTRA neat... if anything, it makes troubleshooting easier. If you can get the correct links for the PDF files, I'm sure someone here (or me) could help you out.
And don't break anything - you don't know hell until you've tried installing a Sustainiac in a non-standard guitar!