Hi, I opened the model and had a look into it.
There are several issues you should try to solve if you want to keep this model:
1. There are a lot of N-gons because of interrupted edge loops and vertices on edges. Don't delete edge loops or part of edge loops simply by marking and "delete" because then the connected vertices will remain and cause N-gons and bad geometry. You should delete via the interactive menu (edge loop => edge loop delete). To clean it up I would use the command merge vertices or merge. With this you move the bad vertices to one end of the edge over a vertices and join it.
2. In the bottom part you have another part of geometry inside the object, which is partly sticking out, I would remove this through cutting away the faces.
3. If you want to keep the shape you should bring more edges/edge loops to the hard edge, but avoid creating N-gons, make all geometry 4 sided (I know its easier said then actually done)
4. The connection between bottom and the wing parts will smooth out different, maybe you can join these 3 objects and connect edges and vertices at the connection.
5. Your bottom part is not symmetric, esp. on the bottom side. I think you moved some things accidentally. One option to fix it, cut the model a long the middle axis in half, keep the half of your preference and mirror the geometry, if necessary rejoin components.
6. On the top part you lost the material, apply again the lambert.
7. When you separated the top from the bottom part, some faces have been left out, which are now laying on the bottom part and produce faces on top of each other.

All over I would recommend to remodel esp. the bottom part, if might take the same time as cleaning it up.
Check for some tutorials in Youtube or better Simply Maya for Modelling, it will help you a lot for your project.
I would avoid at the start jumping between Maya and Zbrush esp. for such type of model. You can produce all shapes in Maya esp. for such a Space Ship.

Have tried to clean up the bottom part.... the way I would do it but its not complete. Also I don't know, why it doesn't smooth out at "3" like the other parts.