I cannot seem to get any audio input or output from my iPhone, I think that this might not be related to the actual parts...

I have bought an iPhone 3GS logic board off eBay and have tried to restore it to the latest firmware, 6.0.1, and receives...

Try pressing the power button AND both the volume buttons at the same time. Normally when this combination is pressed, a bootrom menu should appear. If held long enough, it should reset the tablet and eventually it should boot, just keep holding the buttons.

Hi William, You might not have put your device into Pwned DFU mode. (Google how to if you haven't). The 5.1.1 software is not the latest firmware by Apple, and they do not like their users changing to different iOS's apart from the latest version. Pwned DFU allows you to bypass this safeguard put in by Apple. There are other reasons for this and I will cover them if this does not work, but this seems to be the common issue for people who have not looked into the world of jailbreaking and unlocking. (04.10.01 is your baseband, in case you didn't know)

The LCD could be a cheap £5.00 replacement part bought off eBay. These displays do work but can have faults, like uneven lighting around the screen and dead pixels. The display could be a cheap one.

There is only one microphone on the iPhone 3GS, at the bottom of the device and there are also 2 speakers of the iPhone, the earpiece on the iPhone display assembly, and the speaker, which is near the microphone. The speaker and the microphone are attached to the dock connector assembly. I really have no idea why the microphone only works when on speaker, maybe try a software restore or maybe replace the Dock Connector Assembly?