326 HO, the most likely case is that the tranny and column were changed at some point.

I'd like to believe that it was not the case...

I know the H.O. cars got most everything the 400's did, or clost to it as far as the suspension and upgraded components, so the 3 speed could have been an option ordered?

Have you gotten your PHS documentation? That will tell you everything the car was ordered with.
http://www.phs-online.com/

Let us know what you find!

Brett - 67 Drop Top 455!