After replacing and researching parts, I came to the conclusion that everything I was doing was not fixing the issue and it must be something else.
I've heard theories:
Lower Oil weight to 5w-30 and it will smooth out idle
The M44 simply always rough idles
Vacuum leaks are always the cause of rough idle on the M44
The ignition components used on the M44 are a poor design
The fuel pump causes rough idle before it fails
The cam position sensor is the problem most of the time
Now, these are all solid theories, but are they MY problem?
I can tell you that the majority of the things I was told to do did nothing, but the idle was improved greatly when I was finished.
Firstly, I was a big fan of the Cam Position Sensor theory. It made sense and was a critical engine component for timing. I replaced it and it did nothing!
Secondly, the PCV valve idea sounded good too. It made my cold idle much better, but not the warm idle.
Thirdly, I decided to take every-ones advice and start pulling apart the intake system.
Now, at this point I began to strike gold. I replaced all the upper intake gaskets and began looking through hoses.
This is where I found a crack in all four of the hoses going to the injectors.
The spider injector hose assembly was replaced and it got rid of the flat acceleration. Idle was improved slightly, but not cured.
Fourthly, there is no way in Hell I'm replacing fuel or exhaust components. These things are very reliable and don't fail too often, I've watched countless guys replace catalytic converters and fuel pressure regulators only to have the problem come back in a day.
Another component that often takes the blame is the ECM, this is often replaced by BMW owners. The problem comes back 80% of the time and is clearly a waste of time.