Just to clarify: The hole with the HDD's is already there as I need the HDD's to be in that bay and the drive covers didn't fit. I will etch and light the window so it should look as plain as it does now.
Also the 3 1/4 res will almost certainly go in there with the HDD's....I think
EDIT: Just been speaking to XMS and I may as well stick the pump on the floor and put the HDD's in the spare drive cage. Then the res will be behind the window with an etch and some lights.