110,000k miles, S model, Car intermittently keeps running rough. Keep getting a code for cyl 2 or cyl three misfire, I clear the code and it’s fine for a few days then I comes back. Car has new plugs. Replace the coils the next best guess?? Ideas appreciated

 

Has your timing chain ever been replaced? There is one cause due to retarded timing on a stretched chain. HPFP perhaps. There are many reasons for misfiring. Have you done a full OBD scan with a comprehensive code reader?

 

Before spending money on coils , measure the resistance with a multimeter. Or unplug/swap the coils one at a time and see if you can locate the misfire to a particular unit.

buy the coils with a metal heat shields

 

Timing chain is original

 

Intermediately runs rough. So there is a interval that it runs good!: consistently runs rough; would be a different story. Are the Plugs NGK IR; those are the ones that work for me. You don't want to do everything under the sun you want the simple fix, but there in lies the problem. because simply running it could lead to catastrophic failure.
The Vacuum pump could be going out.
Do you want to fix the problem from advice or do you want to fix the problem using analytics(voltmeter, and exact); if thats the case keep in mind the computer board(on board) tends to fry a circuit between the cam position sensor and the microprocessor When this type and model is at it worst with electronics(from what I have seen on the web).
I would buy one coil and swap one out(mix and match); swapping in the new coil on each of the 4 and restarting the car. Unless you have a expensive Over a thousand dollar OBD 2 Then I would focus the new coil on number 3 and use the old number 3 coil for the 2 or 1. Lower oxygen sensor or wastegate actuator could all do that. A soft diverter might be the origin of that problem. When the vanos goes; well you know; throttlebody could be all gummed up get some 2x2 berkable gum cutter and give it a try! did you change the air filter? did you change the Oil? Have you had it walnut blasted? the Cat convertor is expensive but can cause those known symptoms(never ever use fuel system cleaner on that engine is what mini cooper dealership told me for 2 reasons it's direct injection so those plugging up is not likely under the pressure there at. And also because that cat convertor is super sensitive and in most cases regularly using octane booster additive or fuel cleaner WILL destroy the unit.