Advice on crashing MacPro

Details for the system in question...

Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro3,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.8 GHz
Number Of Processors: 2
Total Number Of Cores: 8
L2 Cache (per processor): 12 MB
Memory: 16 GB
Bus Speed: 1.6 GHz

System Software Overview:
System Version: Mac OS X 10.5.8 (9L31a)
Kernel Version: Darwin 9.8.0
Boot Volume: Macintosh HD
Boot Mode: Normal


So, over the past couple months the situation has seemed to degrade steadily to the point where it now is. Basically, if the computer is left on and left alone for seemingly as little as ten minutes it tends to crash, but not always and not consistently. I cannot figure out what has changed to cause this issue. The system is up to date, and I've tried the following troubleshooting steps.

1. Repair permissions (via Disk Utility and OnyX)
Note: I always get the same list of permission differences and warnings, they don't go away after repair.
2. Uninstalled Apps not in use anymore with AppCleaner.
3. Ran other maintenance tasks with OnyX, such as deleting various caches and the like.
4. Verify Disk checks out OK.
5. Ran TechTool that came with Protection Plan (see failure reports below)

Just today, I had a crash and when I booted back up, I got the folder with a question mark, indicating that the system could not find where the startup files were. No settings have changed with regard to boot. Given the failures on the TechTool, it sounds like it could be a pretty straightforward hard drive failure. So...

I have about 2 weeks left on my Apple Car Protection Plan and I'm wondering if I should just take it in for a tune up and see if they will replace the hard drive under warranty. But, if it's software related, will they just suggest I reinstall the OS? Or upgrade to Lion?

Thanks for any input on this.

TechTool Results (failures only):
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Format Check
Failed
This test establishes whether the volume was properly formatted during initial setup routines.

Since this test uses parameters established by the device manufacturer, this result most likely indicates an actual hardware problem. Consider backing up the device, reformatting the media, replacing the data, and then testing again.
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Directory Scan
Failed
Performs a read test of the directory area for the selected volume.

Media defects cause this test to fail. You should consider backing up the device, reformatting the media, replacing the data, and then testing again.
----
Volume Structure
Failed
TechTool Deluxe can scan volumes for problems related to the numerous structures that are necessary for the volumes to operate correctly. If problems are found, TechTool Deluxe can attempt to repair the damage to help reduce the chance of future problems.

If TechTool Deluxe has discovered problems with the volume structure of a volume, allow the program to repair the problem. Quite often these issues are minor, but sometimes they can be indicative of a more serious problem. If the problem persists, consider backing up the device, reformatting the media, replacing the data, and then testing again.