OK, So I re-read my post and I guess it does sound amusing
Sound through USB is not a problem as it's only used to send digital data. The sound processing takes place in the boxes you add to your system. I have a Sony XA-300 auxilliary input box for my SOny head unit. It comes with USB input and appears to the PC as a USB sound card. The sound quality is fantastic with no chance of interference, whereas audio cables from the PC to headunit are nowhere near as good.
The only downside to what I was suggesting is the D-Link USB radio. IF there was an alternative I would probably go for it but as everyone is building fantastic front ends for it in their software it's hard to move away from it. It's not USB that would put me off purchasing. Take a look through the forums and you will find lots of people using it.
I can't wait to see the final thing. I have no idea if your Aircon control are going to work! But if it's a case of replacing switches then this should be fairly straight forward. I think displaying the feedback from the car to the PC is going to be your hardest task.