DVD Drive dropping off grid, followed by Finder and Disk Utility issues

I'm having a very strange series of problems with my 8 core 2.8 MacPro.
A few weeks back I did a DIY repair/replace of my optical drive. For the last few months it was failing to open when the eject button was pushed. The drive would make a noise as if it was going to eject but it would take more and more time/tries to fully engage. After a few calls to Applecare and a few attempts of trouble shooting I got a replacement drive.
And now I'm having a whole slew of other problems and am at a loss as to what is causing them and how to fix them.
The drive ejects beautifully...for a while. But for some odd reason after an indeterminate period of time (by which I mean it's not consistently the same amount of time), the drive simply ceases to exist in the eyes of the computer. It will not show up in "About this Mac" (all that shows up is a blank screen when I click the "Disc Burning" section of "More Info"). It will not eject any disc that is in the drive (which shows up in finder sometimes...even if it can't be played by the DVD player application). It doesn't show up in Disk Utility.
In fact, after a while nothing shows up in Disk Utility. It gets frozen on "Gathering Disk Information" and doesn't show any of the hard drives (yet all of them show up in the Finder window and on the desk top).
And then the great grinding down of operations goes into full swing - sometimes the finder window won't open. Applications won't quit. Going to the Finder/desktop results in Beach Ball of Death. Yet I can force quit using the Dock. Sometimes I can shut down, sometimes I need to use a hard shut down using the power button.
I have rebuilt permissions. I've used Disk Warrior to rebuild/repair all disks. I've unplugged all external hard drives. And upon restarting, things will work...for a while...and then things start going wrong in a domino effect.
I haven't seen any pattern in regards to programs being used (it doesn't, for example, start after I launch any specific program.
Any ideas or suggestions would be appreciated before I call Applecare again!
Thanks

Thanks for the hard drive tip. I'll see if that helps...
Wish I could tell you what drive I have but today it didn't work upon start-up and I didn't realize it until I started to process/compress something.
Forgot to mention two other things...
1) I did a virus scan and everything came clean
2) This all started last week after coming home and doing an Apple automatic software update. Unfortunately I don't know what it was and not sure if it is linked, as I swapped out the drive right before I left for a long weekend (so only tested the new drive briefly)

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