Don't worry about it, every single 4.6 makes this noise. It is not the shifting that does it, but the way the throttle closes when you either upshift or let off. You will get the same noise if you put it in manual mode, slam on it and let off around 4-5k RPM. I bought the truck from a friend who had it from 10k miles on, and it has always made the noise.

It sounds like a mixture of a bird chirp and a BOV. If that's what you're talking about, don't worry about it. I actually found the same problem on a customer's E55 with a ported throttle body. The throttle plate most likely rubs a little and is feathered closed by the computer so that there is no lurch when you let off the gas.