Just a quick update - more investigations have shown that my Fusion has at least 2 leaks, both into the passenger footwell.
Leak 1 is coming from an internal sealant type joint about half way up the angled section of the footwell. It is only like a pin prick but lots of water is getting through.
Leak 2 is coming from the extreme left hand side under the windscreen heeater vents fascia, from inside a box section that appears to run across to the other side.
Both of these leaks seem to be seen when water is poured down the passenger side of the windscreen. I have removed the plastic thing along the bottom of the windscreen (I think it is called a scuttle). under this is a flimsy seal that water is getting behind.
Will try a letter to Ford hopefully to get these problems sorted under warranty (fingers crossed).