I had wanted to do this myself. What did you use to synchronize the audio and output a master?
The key I think is the correct capture feature. I just downloaded "CaptureIt!" and found it accurately captures the 512x342 pixels and compresses it perfectly. The resulting .mov loaded perfectly into GarageBand and GB output a file that was just as clear as the original. I may look into it as it is shareware.
I am of course assuming it looks pretty much the way it does on YouTube once you export it from your editing software.