Sorry to hear of your problems.
Exhaust Gas Recirculation (EGR) valve is, as the other poster has said, the best place to start. This part was problematic on this engine on early Focus II, but is more reliable in later cars. A competent DIYer should be able to get this out and give it a clean as it can get gunked up with soot. An occasional blast at high revs (e.g. hold onto 4th on the Mway for a bit at above 3000rpm for a minute or two) can help blow some of this crud out of the back.
However, I would be very surprised that this was not the first place a Ford dealer looked, as EGR valve problems were relatively common. Might be worth a second opinion from a different dealer. Or try and find a diesel specialist if the problem is not resolved within warranty. However, because the problem has been reported within warranty, but not been resolved to your satisfaction, I would continue to press Ford to resolve the problem.
I think it's very unlikely to be poor fuel quality. I'm assuming that your reference to the M8 means you're in Scotland. I understand that virtually all road fuel in Scotland comes from the Grangemouth refinery (regardless of brand). Supermarket fuel may be less likely to be contaminated as most supermarkets sell so much, that it doesn't sit around getting water etc in it, and as the Tesco fuel contamination debacle of 2007 shows, I doubt you'd be the only person affected.
2- Diagnostic codes: If the main engine light flashes when the problem happens, it means a code is being written to the car's memory. On the Focus II, the codes stored can be read by using this process. Start with the key in, but don't turn it. Hold down the button on the end of the trip computer stalk, then turn the key as far as bringing on the dash lights (e.g. oil, glowplugs etc). Keep holding it, and after a few seconds, it should go into its diagnostic mode. Press the stalk button again, and it will cycle through various diagnostic tests (e.g. dash lights, gauge sweep, data from key sensors). Eventually, it should display codes like P0123, although if none are stored it will just cycle through all the same tests again. You can then check any that have been stored online, or tell the dealer.
Hope that helps. Let us know whether you get to the bottom of the problem.
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