http://m.youtube.com/watch?v=LQhwrJ_hl4oHi Dave, have a look at the above YouTube link,
It is a video of a Ford Duratec engine and the threaded holes appear to be used to secure the spark plug fittings on that particular model.
'Our' Duratecs have different spark plug fittings so the threaded holes are spare.
You will see the fittings at 1 minute.