I bought the car in April with 26k miles and it rolled over 32k on the way home from picking it up from the dealership after having hit a dear and having both water pumps replaced under the Defect Warranty. When I started it upon picking it up, it stumbled for about 5 seconds before running properly. Didn't think anything of it as it had been sitting for a month, so, went on my way home, over 150 miles away.
Got the car home, put it on ramps and the next day I changed the oil and installed my skid plate. Started the car and the same thing happened. Reset the service light for the oil change, started the car again, and it again stumbled and this time through a engine light on the speedo. Took the car to Autozone and had the codes pulled. Ambient Air Temp (possibly a bad sensor) and Misfire on cylinder 3.
I'm going to have the car transported by Mini again back to the dealership and have it checked out. I'm hoping there is some information I can find here that will help arm me in the event I need it to help resolve the issue. Has anyone had a similar problem? I've found the HPFP issue, but don't know if that is quite the problem after reading symptoms. My car has trouble starting, but then runs fine, attains boost, and drives as normal after a few seconds.

 

I had this problem on my r53 mcs, it was the ignition coil. I no the two cars are totally different but your issues sound the same as mine were. hope it helps..

 

I had my HPFP replaced the other day - the fault code reported is 2880. I'm not if it is similar problem but the it stumbles a few times then loss all power. Mine was running fine for a while after the engine light came on then after a few miles no turbo boost etc. The SA told me it was a fail safe when engine light comes one and it cuts everything back allowing you to limp. This is when the engine light is yellow and when it is red you should not drive the car.

 

It was a yellow light. The dealership had it picked up this afternoon by a flatbed. Haven't heard back from them yet.

 

My misfire ended up being the timing chain issue in my '09 Clubman at 23k miles. Whatever the problem is, Im sure MINI will fix it.

 

Got a call from the SA this morning. Faulty ignition coil. Part should be in tomorrow and the car will be loaded on a truck and delivered back to me Wednesday. That's service!