The Shield Base is still in Beta and for now it takes up a full socket, of which there only two. So if you plug it into any of the GoBus ports on Socket 2 (ports 5-8) you must leave all other ports open. So in your case, if you have the other modules on 6, 7, and 8 the Shield Base can only be plugged into either 1, 2, 3, or 4. But nothing else can be plugged into the remaining ports. Alternatively, if you want to use port 5 for the Shield Base, you will need to leave 6, 7, 8 open, and place your other modules on the remaining ports.
When the Shield Base has finished it's Beta phase, it will no longer take up an entire socket. In theory one could then connect 8 Shield Bases to the Netduino Go.
Cheers,
Steve