That's O.K. to be confused, that's what we're here for. The water pump location isn't critical on these engines because the WP doesn't mount directly to the block, like say... a small block Chevy or Ford V8. The Duratec WPs are mounted to bracketry to the head, or the front of the block, and connected to the block's water passages only by water hoses and/or cross over tubes/etc. That in itself makes this swap very easy to adapt to your needs.
