Nice job shifty.
Suggestion: drill a hole in the mobo tray under the mobo(~1.5" diameter). Than put all the wires cables from the PSU in there. You could also bring all the wires that come from the case and SATA behind the mobo tray and than pull them out through the same hole. Molding around the hole.Link below.
For the holes on the top of your case there is this:http://www.crazypc.com/products/83010.html
Good Luck.