I have had the same recurring problem with my R56, in that every now and again the engine will slip into "limp mode" and I will get 50% reduced power. I have replaced the HPFP which stopped the spluttering on tick over and has helped with cold starts and some flat-spot power problems, but I am still getting the reduced power from time to time.
Along with an oil service, the engine has had a new timing chain tensioner and water temp sensor, and of course the HPFP.
I am boggled as to what the problem could be, my local specialist garage assured me that the problem was down to the HPFP failing. Now replaced, the garage dont have a clue as to what the problem could be, and I dont feel comfortable giving them the car again to try and fix this problem.
I have the car booked in at Lohen next month for a de-coke and dyno test, but above all I just want the reduced power problem to go, so I will ask them to look into that before the de-coke I think. I am also getting a rough idle from the engine, which has made me think it could be due to a large build up of carbon, but not sure if this can cause the reduced power problem I am having.
From what I have learned with owning the R56 for about three months now is that although forum members are saying they are having similar running problems to the reduced power issue and have fixed it, by say, replacing the engine thermostat or M.A.P sensors, that doesnt mean it could be the problem I'm having.
The codes that were being brought up with mine recently where directly linked with the HPFP failing, but there was also another code (I was not given the code itself) that read something along the lines of "exhaust emissions" I think.
From what information I have gathered from 6/7 garages, including main dealers and mini specialists, is that although the R56 has now been around for seven years there are many engine problems that go under the radar, and in that I mean mechanics have told me that if I took my car to a main dealership and it was under warranty they would simply replace the whole engine and not even try to solve the problem by replacing parts. I have noticed in some for sale adds that owners are putting "engine replaced at X miles due to problems". I have seen this in more than one add.
I dont know if what you are experiencing is similar to what I'm having but as it's related to the HPFP failing, and reduced power, I hope it is some help. The only route I am going on is now taking the car to one of the best known mini specialists in the country, and fingers crossed they can sort my problem.