I thought it was worth updating this thread as things have happened.
My engine malfunction was caused by a split in the intake pipe for the intercooler. This was fixed, but not under warranty. They did fix the suspension under warranty and did an ECU upgrade for free too. I can say that the car is like a new car, more pick-up in 2nd gear, no stalling feeling, acceleration is strong and fuel economy is a world different - I did a 300 mile run and it returned 55mpg which was good considering I was stuck in traffic and a lot of the journey was on windy, hilly roads.
This was all done at the Ford main dealer, so kudos to them - was happy to pay for pipe as it seemed fair game for wear and tear. The parts they paid for were more expensive overall.