Why can't my Mac Pro use my hard drive(s)?

Question

Ok, so I'm using a 2008 mac pro (some specifics are listed at the bottom) and I'm having trouble with my hard drive(s). The hard drive I've been using is full, and sometimes the System Information will show that is full of Audio, Movies, Photos, Apps, Backups or it's just chuck full of "Other."
But the problem is that my computer stopped using one of my hard drives a while back. It was called "Bay 5." I've opened up the computer to look at the hard drives and I actually have three. Ever since I lost Bay 5, I lost my Adobe Creative Suite and I've gotten a notification that says "The disk you inserted was not readable by this computer." But the drives are the same type as the Macintosh HD, only with 500 GB each. I've clicked "Initialize" on this notification (sorry, I tried to take screen shots but suddenly my computer says "You don't have permission to save files in the location where screen shots are stored") and it pulls up the disc utility and has a drive called "Media," (but only half the time). Bay 5 is not there and neither is the other drive that's there.
Wow, that screen shot thing is new. Maybe you guys could help me with that problem, too.
I'm lost. I've looked at 15 min. long youtube videos but none of them have helped. I just want to be able to use those hard drives. I've tried holding the D key at start-up so that the computer can do the Hardware check (or whatever it's called) but it just pulls up a flashing folder with a question mark.
I'd really appreciate some help.
Processor:  2 x 2.66 GHz Dual-Core Intel Xeon
Memory:  4 GB 667 MHz DDR2 FB-DIMM
Software: Mac OS X Lion 10.7.5 (11G63)

Answer 1

Buy Carbon Copy Cloner and some new drives. Make sure you have two backup sets and are using TimeMachine as well.
Reset SMC
You have a 1,1 2006 model. It is low on memory, which is cheap at $25 2x2GB now on Amazon
Consider that drives fail and you may have some drives that are more than 4 years old.
If you want, and have the money, consider investing in Disk Warrior 4.4 or 5.0
Data Rescue 4 has a demo and would try to find files, would need a recovery drive volume of course also.
Invest in an SSD for system boot drive, $119 / 250GB, and use a WD Black 1-2TB for data $120, another for TimeMachine.
Adobe CS needs more memory that you have.
AHT is not going to help and is on the OEM DVD with 10.4.x that it came with but what you need is boot from another drive or recovery mode and use Disk Utility (and or Disk Warrior). Single User Mode and 'fsck" is also useful as would Safe Boot. But you need a working copy (clone)  backup too.
I like to have a nice small "Emergency" boot drive with just the minimum for system maintenance, 20GB is fine, some users create a USB flash drive but FireWire or USB2 work well. Or just designate and create a small 20GB volume on any of your other drives.