If you're making it tall enough to fit a 5 1/4" bay then you should plan to allow for a Zorro riser on the left side of the machine to fit 2 or 3 zorro slots off of the expansion connector.  With proper spacing a zorro riser could be created so the slots hang above the 68000 socket.  Of course it would need to be tall enough to not conflict with a 68000 socket accelerator so you could only maybe fit two zorro slots wihtout it getting too tall.  Also punch out holes for DB-25, DB-15 (vga), USB etc.