I installed an aFe air intake and my 2000 328Ci makes a whistling noise when "coating" (low-mid vaccumm in the intake manifold). If I accelerate or decelerate the whistle goes away .... the noise seems to come from under the car. If the original air filt/box is intalled the whistle goes away. If I remove the original air filter/box from the mass flow sensor and run the car with out an air filter the whistle is back. Did the same thing with my son's 2001 330Ci and his does NOT make the whistling noise. All this makes me believe that there is a vent valve in the air intake manifold or a small air leak that once the vacuum pressure in the manifold increase it closes and the noise is gone. This thing is making me crazy and no one has been able to tell me what is wrong. Took the car to the BMW dealer, thye checked and smoke tested everything and all they could say is ...we put the original air-box/filter and the noise is gone.
^^^ *smartypants* I don't know about a vent valve, my guess would be an air leak. I've never tried it, but one thought I've had to move air through an engine is leave it in gear (obviously engine not running) and duct-tape a shop-vac to the muffler pipe(s). Less complicated if you have one exhaust exit point vs. two. Having never tried it, I _don't know_ if it could cause any damage to anything internal; you'd have to open any valves in the intake path - no constraint with the MAF, I think there's just the flap in the throttle body. If the E46 throttle isn't cable-actuated, you'd have to figure out how to get it open. Since an engine is basically an air pump, as long as the complete air path isn't blocked and the transmission keeps the motor parts from being able to move from air pressure, theoretically, it should work. You'd have to ask someone who knows the airflow rate/capacity of the engine whether a shop-vac of any particular size might push or pull enough air to cause a problem. I would also call aFe and ask for suggestions - if it's a common problem, they should have encountered it already.
I have the same intake on my 2005 330i and a friend of mine has a long tube intake on his 2003 330i and we both have a whistle. I believe it just has something to do with no more sound insulation from the OEM airbox. The OEM box is designed to be quiet hence no growl like you get with an cai either. Neither of us have had any ill effects and personally I think it sounds kinda cool.
I use to have a 330i with the dinan cold air intake and I had a whistle issue and I found that my intake boot to my IAC (idle air control valve) was torn slightly causing the noise. Later on the noise returned and I did find that the DISA valve in my intake manifold broke replaced and no longer had any whistle noise. AFE intake is a great upgrade and I personally like the sound note