OK. I would check the rubber boots again, just to be sure (the accordion ridges). If everything checks OK, you might want to see if you don't have a leak at the DISA level. The DISA has an integrated O-ring, with a very small rib. The rib fails prior to 70 k miles, and small vacuum leak is created, which could also cause a whistling.
The DISA valve itself, fails at around 100k miles. It has a plastic/nylon rotating axle, that will get eaten up in time, and the flapper that controls the air for low grunt doesn't do the job anymore. Also, the top steel pin loosens up and can fall in the engine, ruining it (GAS has a repair kit, which is much cheaper than a new DISA valve - I have that one in my e39, and it's working better than a new DISA).
The problem if you remove the DISA is that there is no replacement O-ring to seal the valve. If you get the DISA repair kit, you will get a replacement O-ring. You could also go online or some hardware stores and find an O-ring similar to what GAS sell - they are cheap, but you have to make sure they are heat and hydrocarbon resistant. The old O-ring, which is probably toast, you will have to scoop it out with a pick or a small screw driver.
Another location could be a torn plastic CCV hose. To change the CCV, it's a royal PITA, because the space is small, and there is a certain procedure on how to attach the upper hose that goes from the intake manifold into the CCV and is routed between the intake manifold and the distribution piece at a certain angle. If you need help with that, I can link you some references from another BMW forum or 2.

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Stable: e92is, e46 M54B25, e83 N52, e53 N62 - sold, e39 M54B30 R.I.P.