I'm also got a kind of custom setup.
Honda Civic Stock Stereo -> CD Changer to Aux Input Adapter -> 3.5mm to 2.5mm adapter -> 2.5mm input on HTC Y adapter.
Belkin Cig. Lighter to USB Female Port (From old iPaq) -> HTC Stock Sync/Charge USB cable -> MiniUSB input on HTC Y adapter.
So, when both the power and audio are plugged in, I hear a horrible hiss on my car stereo, not to mention a sound that varies in pitch to my throttle. When I unplug the power, the audio is completely clean. To me this seems like some kind of a grounding issue - to say that the Audio and Power both have seperate grounds, and bridging the two creates a potential difference in the form of noise on my Sound. Also to note: I only hear the noise when the Y adapter is plugged into the phone. With the audio and power plugged into the Y adapter, but the Y adapter not plugged into the phone, It's perfectly clean. I'm kind of baffeled.
The only solution I can think of is to gut the Belkin Power->USB adapter, and providing it from 12VDC elsewhere. I've got a tap directly below my passenger seat where I have a big power inverter tied to my battery. I don't know if I'd hear the same sound by grabbing my power from there.
Anyone with an engineering mindset have an idea? I'm open to suggestions.