We have a couple symptoms on our 2011CM w/ 60k on it.

1. Some mornings, it will run really rough at start to the point the check engine light comes on. It doesn't stall and it clears up after a few minutes. This will throw the following novel full of codes:
P0415
U1F03
P0003
P0103
P02AA
B2AAA

2. On moderate to hard acceleration, it will stutter, sometimes pretty violently.

When I first checked the codes, there was another one that mentioned timing and another for a misfire on cylinder 3. I tried new plugs and coils. Strangely, issue 2 seems less severe, but not eliminated. Any ideas where to go with my troubleshooting other than the to dealer?

 

I haven't looked up the fault codes, but my initial thought is suspected injector leak.

I'd check if the plugs smell like fuel. Try checking before running the engine, or whenever you feel the misfire is imminent. If they're dry before you start the engine, run it for about 20 seconds with your spark plug socket on standby, then shut it off and immediately remove all plugs to check for fuel odor and/or wetness. The according cylinder is likely to have a leaking injector. In which case...dealer. At least this way you can get an idea beforehand.

 

A reputable Mini specialist if you can't or don't want to try chasing it yourself. I try to stay clear of dealer for most out of warranty issues.
Codes sometimes lead you down expensive paths to nowhere but out of pocket expenses.

 

How olds your battery. A bad battery can still start the car but won't have sufficient power to run the ECU, modules and engine management systems which will cause the car to run rough give multiple codes and do strange things.

You could go to a department store buy a battery and keep the receipt if its not the battery, a dead give away is losing time and date on your dash.

 

fault codes:

P0415 Secondary Air Injection System Switching Valve "B" Circuit
P0003 Fuel Volume Regulator Control Circuit Low
P0103 Mass or Volume Air Flow Circuit High Input

I don't have the listing of the other three codes, but it looks like it might be related to something going on with your intake flow (like a cracked air horn or maybe a rubber boot is not seated correctly) this would effect your fuel air mix. I would have look up the other codes and go from there. If it is the air intake side I would more than likely do something like a smoke test to find the cause.

Best of luck.

Motor on!

 

So here's a fun one. My first step was replacing the plugs. After that my symptoms didn't change so I kept on troubleshooting and I replaced one coil then the rest. I took it to a bmw/mini specialist and they found that Napa gave me the wrong plugs. They put in the right ones and everything is good now. So plug replacement cost me $600. Maddening.