Okay, I think I've narrows down some issues with the audio. In CodecCommander's Info.plist, I set <key>Check Infinitely</key> to true and that seems to have fixed the random dropout, but not the lack of headphone audio at boot. When I wake from sleep after this modification, headphones do work.
It would seem that <key>Command</key><integer>27723556</integer> is being passed at wake, but not at boot. Even when I set <key>On Init</key> to true, it won't work until I sleep and wake the machine. But this seems to do the trick.
Any idea how to send this command at boot?
EDIT: If you boot without headphones plugged in with <key>Check Infinitely</key> set to true and <key>On Init</key> set to true, then headphones will be detected automatically and function correctly. I have heard static after sleep in this configuration however.
I've also modified an alfred script to unload and load CodecCommander.kext
Fix Audio.zip