For the tranny, if you have an ATX, the newer the better. They made improvements to the CD4E each year. Ebay has rebuilt CD4E's for around $800 without core.
Why the aversion to car-part.com? LKQ in AZ has various low-mile Focus Zetecs for a whopping $350. For that price, you could buy two and mix and match.
Right here. I just did a search for '00 Ford Focus engines.
HTH,
Ben