It's still going to be a huge mess to put together. Even combining everything into one one object will be a monster of a task to sew together with automapping, unless your going to extract certain parts of the geometry, and then your still going to have quite a bit to sort out even at that.

Try automapping what you have and show us the UV layout.

EDIT: I believe I understand now how your going to automap. I remember seing a Rebel Blockade Runner done in the same fashion as your Star Destroyer. All the micro models were independently uv mapped and textured, aswell as the main mesh.