It might be easier to just make a frame to fit round the hole with a new primitive (by extruding the shape from a cube or booleaning another cube, not a big boolean fan myself as can they do really weird things, but a frame should be easy to make from scratch).

Extruding it all from one thing might make things a tad complex when it comes to uv mapping it all, plus if you have seperate bits and they go wrong it isn't such an issue.

Incidentally for extruding practice the tie fighter tut on this site is really rather good. First thing I ever made that wasn't a gun(nostalgia!) and it's very good with all this moving extruding lark.

EDIT: had another random thought which was that sometimes when you extrude or boolean things from a very large single face you get stretching and shadows because the geometry has to try and adjust itself over such a large area. You might try starting with a plane or splitting your cube a little more before booleaning it to avoid that.