I had a similiar problem that lasted for a few months. The hard drive would be gone and come back. I started leaving the computer on all the time so as to avoid the problem otherwise 4 to 6 tries to get it going. One day I took all the hard drives out and put only the offending hard drive in with a new cable and now it works. I haven't had the problem since. I hope you are as lucky.
I also have had problems if the room was too hot or humid. I once lived nearly on top of a lake and my computer broke down more that year then ever before. I think it was from the extra moisture from the lake. Happy to have moved. Good luck again.