Ok well after doing a bit of research it seems if you have a problem with your bluetooth system for your D3 the solution is quite simple. All volume controls for the system should be able to be controlled threw the volume knob on your D3 this is not a separate system like the voice guidance volume. If this is the case then you need to switch the IP-bus port that you are using.
So lets use and example to make things easier. You pluged into the IP-bus out on the bluetooth unit and from there you are pluged into the back of the D3 unit. Your phone connects and the D3 Unit recognizes your phone. You make a call and the person on the other end can hear you but there is nothing coming from your speakers from them (this could also be reversed, you can hear them but they cant hear you). All you need to do is switch the IP-bus port on the bluetooth unit. Switch it from ip-bus out to ip-bus in.
This could also be switched where you start of with the ip-bus in and things don't work as well. When i talked to pioneer about my problem they said that if the unit you purchased was programed wrong then sometimes the ports can be reversely polarized (reverse polarity).
I guess this makes sense but you would think that pioneer being such a large company would not make mistakes like this!
Bottom line is my problem is fixed!