First things first: I fixed it!
It turns out that the UV maps were being incorrectly flipped along the x-axis which caused the objects to receive the wrong parts of textures from the texture files. I dove into the python files and found the culprit: line 237 of the import_craft.py file.
Originally the offending chunk of code looked like this:
if "_fixed" not in obj.data.uv_layers.name:
for uvvertex in obj.data.uv_layers.active.data:
uvvertex.uv = -uvvertex.uv + 1
Notice that negative sign in front of the uvvertex.uv in the last line? That's the problem. Just get rid of it and your UV maps will be correct! I'm guessing that it was originally a workaround for some weird KSP texture handling that got fixed in some update.
So, to reiterate, remove the negative sign in front of uvvertext.uv in line 237 of import_craft.py to fix the texture problem.
Now that this is fixed, I'm going to play around with it some more and finally realize my dreams of creating a decent rocket launch in blender!