I had a similar problem with my E92 3.20D last year. There were strange (rattling) noises coming from the engine. I went to dealer and told them to check the engine. They couldn't find any faulty codes and said : "its the traditional sound of BMW engine, nothing is wrong". After 2000 kms the engine stopped while I was cruising around 120 KM/H on the road. They towed the car to the dealer and couldn't find whats wrong with the engine after inspected it nearly one month. Dealer sent some photos to the BMW AG (Germany) and they sent a new engine for replacement on warranty. After the car repaired I sold it and got the M3.
But now what I am reading is very sad and alarming. My car has no speed limitor from factory (I got M Driver's pack) and I generally do high speed tests (go over 300 KM/H on the clock). If the engine is not that reliable I don't think what I am gonna do if the same thing happens to me since my warrant is over now.
And also those service technicians here in my country don't have enough knowledge both about BMW engines and BMW cars. If I face with any problem about my car, I wrote directly to BMW AG (from their web) and they immediately contact with my local dealer and tell them the instructions. I told them to change my 6MT gearbox oil on my break in service and they refused to change because its unnecessary. I insisted but they didn't accept. Then I wrote BMW Germany and they called the dealer and told them to change my gearbox oil
At least, you could write or call BMW AG about the problems you have with your local dealer before you do anything on your engine. Anyway, what is done is done and I hope you figure out the problems... And its also nice decision for you to stay away from BMW in the future..