"Here's where it gets weird; It decided to boot up all of a sudden and was working fine, so I decided it must have been the cables so I swapped them around.. Booted up fine with cover off and hard drive in place so I shut down and put the cover back on..

Turn PC on.. Won't boot! I take the cover off, boots fine"

Sounds like the cover causing interference to the cables. Have you tried to organize the cables by twist tying them together so as not to be against the cover when you put it back on?