UPDATE- I spoke with Otto's BMW in West Chester PA who sold me the car. I have an appointment on Friday (with loaner car) me to drop off the car and they'll fix whatever the issue it is. They said it's a regular thing and should only take a few hours to fix. I can't wait to see what the car feels like when I get her back afterward!

 

Definitely check your injectors and HPFP first through the dealer, if that is not the case you should check the coil packs. I had the same issue and after the pump and injectors where replaced I was having an issue with one of the coils, replaced all of them just to be safe and the car felt great afterwards.

 

I brought the car in today and met with the service manager who said they are going to do a full check up on it. Apparently it already had the valves cleaned 2 years ago so they put in new plugs. They took it out for a test and still doing it. He told me they looked in the the valves and they are carboned up again and they're going to have to keep it the weekend. They gave me a 2012 335xi coupe to beat on over the weekend though. I just drove that 80 miles back home and I like my 5 year old 535xi alot more than the coupe I'll keep you all posted. Definitely A++ for the dealership though for taking care of me!

 

I picked up the car this morning and all is good. To keep it short the dealer did a complete diagnostic and found it to feel like a slight misfire on the initial test drive. They replaced the spark plugs (I saw the the plugs were replaced exactly a year ago (10,000 miles ago) on the car fax, but it says on the repair ticket (CBS data states spark plug replacement was due)) and took it out again and they said the issue was still there. It felt "heavy" on acceleration. They then removed the intake and found large carbon deposits on the back of the intake valves and in the intake port area. they cleaned all 6 cylinders (didn't say by what method) and also replaced a section of vacuum hose for the waste gate control valves. They did a complete vehicle diagnostic and and everything checked out fine. The HPFP was already replaced 15,000 miles ago and that was fine. They stated the fuel injectors were also showing no trouble codes. They also topped the oil of with 1.5 qts since it was a little low. I'm very pleased with the way I was treated by this dealership and I love this car! I would love to see what the bill would have been if I had to pay for everything! Thanks for everyone's help with diagnosing the issue in the beginning.

 

Glad everything is sorted out.
I would recommend still getting the engine carbon cleanup done if it has never been done. Got mine a couple of months ago and it was a big difference in idling, early acceleration etc.

 

It was done. The dealership cleaned out all of the valves.

 

My 545i (147k) recently had this pulsation stutter on a long distance drive of 400 mls each way. This stutter only happened at high rpm. The following day I got a check engine light. I rushed to dealership but I could not get seen. The SA said it could be injector, coil ect. and he assured me it would be fine to drive it back on my long distance drive. I procrastinated until I got a blinking check engine light (WTF) one block away from home. Worst power loss my car had felt plus pulsing and stuttering. Car was inoperable with loud knocking engine noise that I could hear in cabin. I had the car towed to a indy shop the next morning waiting for the damage, turned out to be bad coils. Cost was relatively cheap. No joke my car has not felt so smooth, quiet and responsive in years.