Tim,
I played with your model for awhile trying to figure out why it wan't enclosed and found myself wondering if Booleans weren't working. So... I shelved your model for the time being and started a simple model from scratch to make sure.
Sure enough the Booleans work.
In the Tech Ref it states "The rules for Boolean operations are strict..." and they aren't kiddin'.
Attached you'll find a simple example of what booleans can do if the meshes are closed.
You can get Booleans to work sometimes without strictly following all the rules... but you shouldn't.
The example contains:
Example project file
Two Bones (one a boolean cutter with all the cutting forms assigned to it- the other assigned to the mesh being cut)
Various Groups all assigned to the Bone that cuts (except the main unibody wing).
Each group a different color. (it could also be a different material or image)
I've included a shaded wireframe image to demonstrate even cylinders capped wiht 5 point patches at the ends work fine.
No need for multiple bones either unless you want to animate what is being cut. (REALLY COOL SFX CAN RESULT)
Note: I've intentionally placed the two odd shaped cutters on the edge to demonstrate they cut cleanly through the wing on edges with no artifacts.
While I need to look at your model again I'd say your wings and/or your cutter objects aren't closed off enough.
If your patience can take it I would suggest remodeling and trying to standardize on 4 point patches.
In my opinion the knowledge of Booleans will be worth it in the long run.
Note: You've modeled parts of your wings that you can probably cut out as well.
If you know you are going to use Booleans from the beginning take advantag of that. Keep the forms simple and cut... cut... cut.