my god man thats huge!
#1 you could cut down on the size by mounting the hdd on the lid, so that when it closes the hdd sits above the mobo. then you can run two fans (intake and exhaust) move air across both of them, have a low profile (server) heatsink and fan. put some soffets (holes in the board) to ensure no pressure problem with the fans.
#2 Make a simple bracket to raise the drive to that height, you can use 5.2mil Lauan to keep the whole wood thing going and some square dowel, use wood glue and brad nails. Total Cost is about $15. OR you can heat up some plexiglass and bend it and screw it into place (pre-drill first) Cost is about $10.



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