What are you planning on cooling with water?
One thing I can see that might work is to put a double 120mm rad like the swiftech MCR220 in the top of the case. Move your two optical drives down to the lower 2 bays. The rad and fans would probably fit there, might not be a lot of room though for airflow, but it may work. I would mount it with the rad against the top, with the fans next, blowing down into the case. If you need more cooling capacity, mod the back of the case to fit a 120mm fan instead of the current 80mm and put a single 120mm rad back there along with the double in the top.
As for res and the pump, put them where they would fit best.
A totally internal loop in that case will be really tough, but I think it is possible if you plan it out really well. 3/8" tubing might be better here simply because of space constraints, 1/2" or 7/16" might not fit too well.