2008 Clubman running rough

Need Help! 2008 Regular Clubman with 65k miles, after about 30 minutes of running the car wants to stall at redlight or when slowing down, sometime the engine light will flash on. If I park for 20 minutes the problem goes away until I drive for 20 minutes again. Took car to dealership, changed plugs, coils, and cleaned injectors, code was #2 cylinder misfire, compression check showed no problems! They dealership wants to pull the #2 and cylinder and want 1500 dollars but will not promise this will fix issue! ANY help would be greatly apreciated! FYI car only started doing this after dealer changed thermostat and water pump due to engine light 3 months ago! I originally though I had gottne some bad gas, has been getting steadily worse, no coolant leak, and the dealer also did a smoke test with no bad results.

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[Nick at Pelican Parts]

If engine compression is good across all cylinders, perform a fuel system test, check fuel pressure, volume and quality. Monitor fuel pressure when good, then as the problem develops. Look for a change. I would start here as it is an easy test to perform.

- Nick

[Dave at Pelican Parts]

One possibility if this is an "S" model (turbocharged and direct injected) is carbon build-up in the intake ports. I don't know how you'd tell if that is the problem short of removing the intake from the cylinder head, though.

--DD