You would need to get a codec dump from your audio hardware to fix the outputs mapped to the wrong ports. Also you could try using this modded version of VoodooHDA by Slice that lets you remap the ports too, it could be easier than patching AppleHDA from scratch.
Also I'm curious too, I was assuming Windows 7 didnt support installing to a GPT partition even in 64 bits variants, what method did you use?

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AsRock P45TS | C2D E8200 | GeForce 8600GTS
Mac OS X Snow Leopard 10.6.1 + Windows 7 Ultimate 6.1.7600 + Fedora 11