As in any classic adventure game, you use up all of the duct tape and glue sticking the two shuttles together. You need a different solution for the new problem.
Thinking outside the dodecahedron, I even came up with ideas including:
1) putting the crew into an industrial dehydrator.
They get dried and preserved, you get their fluids as potential fuel, and when you get a new ship, you just add water and presto, you get your crew back.
2) Cryogenically freezing the crew.
The ole snap-freezing them. Then if you put them in a radiation-shielding blanket on the outside of the shuttle, they'll be kept at only a few degrees above absolute zero, and safe from radiation. When you get a new ship, you pop em in a cryotube, re-animate them and they're good to go (mostly).
o3) The Futurama head approach
Preserving the heads of the crew, and rigging the shuttle to interface with said heads is a very efficient way of having large crew yet small space. The bodies can be stored in some locker back on your home world. If you're into boarding enemy ships, you'd use modified Templar armor that act as robotic limbs for the heads.
4) I saw it once on Stargate - putting multiple personalities into one body.
It's very efficient because you gain all of the collective goodness that are the minds of the people, but only need to sustain a few bodies. You can get a specialist weapons operator, engineer, soldier, navigator, cleaner all in one body!
