First: IP-Bus cable may have been going to a satellite translator/tuner box or cd changer, who knows though. The 2 wires on the IPOD adapter, when connected to vehicle power will allow the Ipod to charge while connected.
Second: Connecting to the VSS wire is to make the navigation function. This may or may not be necessary depending on what the head unit is capable of using to track motion.
Third: The connection to the hand brake is for the video enable wire so that you can't watch movies or possibly access certain menus while driving. Basically is just gets grounded when the brake is applied. It sounds like the prior owner did not like this restriction so he just connected that wire to the ground wire on the connector which works for many brands to bypass the safety feature.