Problem Solved! Here is what I learned, I hope it is useful. Remember, this is what I was able to experience in my specific case, if I am wrong about anything please let me know:
1) Our N54's come with poorly designed injectors that WILL fail eventually
2) Refurbished injectors are a risky item to buy. They could be far off their factory printed specs (which are coded in the ECU), and could have swollen seals that will fall off upon installation and perforate your cylinder head.
3) Our N54's are famous for slightly rough cold starts and sometimes idle. Not something to worry about according to my BMW specialist. Some light and very rare vibrations are normal for our engines. HOWEVER! If you are getting substantial misfires in the morning, along with gas smell, or constant rough idling with poor gas mileage, time to check your components (Procedure described bellow).
4) If you are experiencing any sort of misfire on this engine do the following trouble shooting order to avoid spending money on unnecessary items:
- Step 1: Check for codes. If misfires are isolated on only one or some cylinders, swap coils to see if the code follows the move. Procede to do the same with spark plugs if that doesn't work.
- Step 2: Identify if all of your misfires are on a single bank. If they are, check your O2 sensors, bank-specific vacuum lines and such.
- Step3: If your misfires are in all cylinders, or several cylinders not depending on coils or spark plugs, use INPA or any other BMW software to reset your adaptations. See how it responds.
- Step 4: It is time to check your valves for carbon deposits. Remove the intake manifold to visually inspect the valves. If they are covered in carbon, it is time to clean them. I cleaned them with carb cleaner and a brass brush using my drill. However, walnut blasting is the best way to do this.
- Step 5: Suspect your injectors! Check the index #. Anything under index 10 is likely to fail. pull out your spark plugs and smell them for fuel residue. This will reveal if you have leaky injectors. You can also use a wooden stick or long flat head to listen to each injector ticking with the car on to see if any of them is firing differently.
- Step 6: if you have new spark plugs, good coils, clean valves, new injectors, and have checked your O2 sensors. You can check the following components:
1) Injector coding values (sometimes they fluctuate after inputing them. +-0.02 fluctuation is ok.)
2) MAP sensor
3) Throttle body cleaning
4) vacuum lines
5) fuel pumps. especially HPFP.
6) Engine mounts
In my case, the problem ended up being my new spark plugs (believe it or not). I got a pack of 6 BOSCH OEM fro amazon for a suspiciously low price and was getting misfires. I did ALL THE THINGS I mentioned before and the problem was not fixed until I changed them for dealership BOSH plugs. I guess at least my car won't have problems for a while!
Please let me know if you have questions, or anything to add.
