MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I just finished building mine, and I had a similar question to you.
I ended up just using a thin metal rod (even coathanger wire would work) cut to be the right length, and so that the end of it just ends flush with the hole on the bottom of the body.
Then, the little cylinder that connects next to the trigger, covers the hole and prevents the metal rod from falling out.
I ended up taking a longish metal spring I had laying around and screwing it onto the back of the magazine holder, which keeps it pushed out normally. It worked great actually.