I would definetely keep the front as intake on the last diagramm you drew, I think the 120mm fan would simply blow hot air on to the GPU, and keep the HDDs cooler.
Maybe I'm suggesting a huge stupidity here, but what would happen if you...
It does look a bit unbalanced, but a positive air pressure does help prevent dust build-up. If there is enough mesh on sides/back, I wouldn't change anything, if not, consider turning the side fan to exhaust.
I'm not sure about using the...