Thanks for the suggestions there, much appreciated.
Our local mechanic may have just meant the gearbox is wrong, or I may have misheard what he said, but either way we're in the process of arranging to take it to a Ford dealer now, just so we have some confirmation and hopefully a better idea of what's gone on before we go back to the dealers. The dealers haven't actually seen the full list of things wrong with the car yet, they only know about the engine/gearbox being potentially mis-matched. I have managed to find what I believe to be the engine number, but Ford will confirm this no doubt. If what I found is the engine number then it doesn't match the HPI check we did ourselves yesterday, but apart from that there doesn't appear to be anything else suspicious with the results.
On the day of sale, the dealers told us that the car was clean with absolutely no issues whatsoever, fully HPI checked, no accidents, good engine, warranty, etc, and being the fool I was I believed them and the illusion they presented. If I had taken just one look underneath the car, I mean actually under the engine, we would not have bought the car as it has more leaks than I have ever seen on any car, I don't know how many different fluids there are in a car but I would guess this one is leaking a sample of them all.
When I have the full list of things wrong with it typed up, hopefully confirmed by Ford, I'll post it here for you all to see. The engine and gearbox appear to me to be the worst of the issues but it does have quite a few other things wrong with it. From looking at the body of the car and the interior, plus it being a nice drive, you would never believe there is so much wrong underneath.
On top of all that I've been ill for about a week now but yesterday I woke to find my face was swollen, and it's even bigger today! I look like the bloody elephant man!