3.5 hdd yes if the radiator+fans are not too thick.Thanks for answering! in regards to number 5 would a 3.5" HDD be mountable? Also You would be surprised about the ventilation on that case. If I remember correctly it was based on the Silverstone RV02/FT02.
Lastly...this might be a bit radical but have you thought about incorporating a low profile horizontal backplate for the lower section?
Sorry but I don't really understand the last question, could you maybe make a sketch in paint?
Oh and I started working on something to help with renders, I think you will like it: