I am going to answer all of your questions per my memory and I think all of answers are in the movie itself -
The Alien created a device, from the various stolen electronics, and attached it to the base of the tower, which attracts metal devices towards the water tower. The alien doesn't want to attract metal but wants to collect all his cubes.
The military didn't leave the cubes around in the town but they are trying to research the cubes' technology. The train crash is the reason for the cubes to be distributed in town but most of the cubes are still with the Military.
The Alien is trying to create a device which acts as a magnet to attract his cubes from all around the town.
I didn't get the 4th question, so I am not able to answer it.
The cubes are all responsible for making his ship. It's as if the alien has all of the pieces of cubes to easily make a ship.