I built the audio circuit and wired it up. I also wired the c45 and c46 connections into pins 16 and 17 of the nes connector (these pins are unused they normally go to the expansion port and that's all). I modified my famicom to nes adapter to connect pins 45 and 46 to nes pins 16 and 17 and it works great. I can stick a famicom cartridge with upgraded audio into the adapter, plug the adapter into the system, and get amazing quality audio with the upgraded audio mixed in. Keep in mind that the upgraded audio will only get mixed in when the system is switched to kit audio mode. Unfortunately there's no way to get powerpak extended audio without either building an adapter for the powerpak out of a game genie or soldering inside the powerpak which I don't wish to do:
All that's left to do is wire the outputs into headers and connect them to the multi av port at the back. Then I just re-install the heatsink close the case and this awesome system's done. Oh yeah and I have to wire up the audio switch which will be easy for this system.