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2003 Cooper S misfire

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afternoon folks,

Hope someone can help out, as neither my wife or i are mechanically minded.....!!

She has a 2003 Cooper S, on which the engine management light had come on a few weeks back.
It was registering a misfire on cylinder 2.
After checking it, the RAC guy thought it was the headgasket.

We've had it taken to a friends garage, who after working on it found numerous issues (she's only had the car 3-4 months).

1) compression was down on cylinder 1 + 3
2) someone had worked on the engine before and had split/pinched the inlet manifold seal (and replaced some other seals/o rings that were leaking). Car was leaking air badly it seemed.
3) Water pump was replaced
4) think they checked and swapped the plugs/coilpack with another just to test and it wasn't that
5) The garage we bought it from then took it back recently and had a workshop look at it. They replaced the headgasket, and have had the head skimmed. They have also replaced 2 x engine valves as they were damaged?

So, they are closing up for Xmas. They said the car runs perfectly now, but it still misfires on a cold start and they can't quite put their finger on it.
The car doesn't register any new codes (they took it to BMW and got them to plug it in).
Doesn't need a software update from BMW apparently and the piston rings were not damaged

Any ideas as to what might cause it to still misfire?

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