3D Work Update

I thought I would give a quick update on how my 3D work is progressing - or should I say how it isn't. Over the last couple of weeks I have been having increasingly annoying technical difficulties when trying to put all the pieces together. This is mainly in tihe form that "flipping the normals" keeps breaking - I select the entire box to flip them but when I click "Flip Normals" only a small portion of them flip even though I selected all of the faces. When I try to fix the normals it keeps repeating the same problems it just flips random normals even though I select specific faces. This is making it impossible to continue on that particular save and so I've had to restart several times now with several hours worth of work time wasted.
Physically my section is probably the easiest to make out of all of them, its just flipping the normals and sticking all the pieces together that is creating all of my problems.

Hopefully in this afternoons 3D class I will be able to progress further than I have manged to get so far.