Just wanted to reply so that if someone searches they have the answer to my encounter with the problem...

For the first code about secondary air the hose leading into the wastegate bypass valve was virtually torn almost clean through where it connects. The other end was also worn. I am trying to find my camera to post a picture of the hose and the tear for an FYI. Apparently their master tech said that this could have cause the brake boost code as well...however, the problem would have probably triggered during cold weather starting so I have to see how it handles in the morning. The Gear Recognition signal I have not diagnosed as the code seems to disappear on its own however should it need replacing the dealer said they would goodwill it...