I'm not sure I follow what you're missing. The VSS, reverse, and parking brake wires will not be in the head unit connector. You need to locate them elsewhere in the vehicle and make your connections there. As was said, you can ignore the VSS on that unit. I actually have that exact same unit in my truck. And you can ignore the reverse if you're not using a backup camera.
Grounding the mute wire only applies if you've moved the pin to do the bypass, in which case you'd also ground the parking brake with it.
Are you burning the nav disc onto a CD or a DVD? I'm pretty sure it needs to be a DVD, not a CD.