MOT done. I can now add 2 rear suspension arm bushes to the list at £740 (apparently they have to replace the whole arm, not just the bushes - WTF?). Oh and there's apparently some play in the anti-roll bar too. Yay
On the key front, it must be the pickup hence me thinking its a bonding/paring thing.
Thanks jeebowhite for the tips. The problem with the exhaust was that the pipe rusted through where it meets the back box (so the whole back box fell off). Also because the car was at that point just under 3 years old, ford hadnt released the designs etc for them so no 3rd party ones were available, only original ford once (hence them feeling they could charge so much!). Thats why I ended up searching for custom made ones and luckily found a place near work doing stainless ones!
With regards the remote, its the 3 button flip-key type. My first thought was that the microswitch had gone (as thats the only "mechanical" part) but it just cant be. NONE of the 3 buttons work/do anything. If I then use my wifes key to remote unlock the car, my remote then works every time, all 3 buttons for a good few hours. I can only think its some kind of pairing/bonding issue (I tried some tips I;ve seen on quickly turning the ignition key 5 times quickly but it didnt help).
Fingers crossed for tomorrow but if they come out with any issues & prices similar to their exhaust quote, its going somewhere else!