Backup or Clone Stalls at about 200GB and other problems

Question

I cannot backup more than about 210GB out of 440GB on a 500GB boot drive. I have tried Disk Utility to create a clone of my boot drive and I have tried SuperDuper! to do the same thing. I have tried creating a clone on another internal drive and I have tried to create a clone to an external drive. No matter which drive or disk software I use, the backup proceeds quickly (25 to 50 MB/sec depending upon the drive) until it reaches a little more 200GB, then the backup stalls. In the case of Disk Utility, all of my Application and Library files are captured correctly, but my User files are not. SuperDuper! Starts at the bottom of the drive directory and captures most or all of my User files, but SuperDuper stalls when it reaches the Application and System files (including Library files). In both cases, as I mentioned above, 205GB to 212GB are transferred before the backup stalls.
My hardware config is just below and other symptoms are shown below that.
2006 MacPro
Model Name: Mac Pro (September 2006)
Model Identifier: MacPro1,1
Processor Name: Dual-Core Intel Xeon
Processor Speed: 2.66 GHz
Number Of Processors: 2
Total Number Of Cores: 4
L2 Cache (per processor): 4 MB
Memory: 10 GB
Bus Speed: 1.33 GHz
Boot ROM Version: MP11.005C.B08
SMC Version (system): 1.7f10
Two 1TB Drives configured as one 1TB RAID Set (software RAID)and used for Video and Photos
Two 500GB drives. One is the boot drive and one was being used as a Time Machine backup drive until I started having problems.
• Apple’s “Backup” Software does not complete a backup designed to copy Microsoft Office and Apple iWork files. The software scans more than six million files (there are only 900,000 files on my hard drive) and then fails.
• The computer will not boot from the Mac Pro Install Disk. Every attempt leads to descending dark gray scree with the message, “You need to restart your computer.”
• I cannot empty the Trash. I usually keep Trash empty, so there are never very many files in Trash. Recently I tried to empty the trash and the system started to count files to be removed an it quickly reached one million files after which I “Force Quit” Finder to stop it.
• My computer was going to sleep frequently despite Preference Settings designed to prevent any sleep at all. I thought this was interrupting the backup processes, despite the fact that SuperDuper, at least, seems to stave off the computer’s attempt to sleep. I installed Caffeine and that stopped the unrequested sleep behavior, but did not solve the backup problem.
• Recently my computer failed to find the boot drive. When this happens I can hold the “option” key during boot and select the boot drive myself.
• I have reset the PRAM and VRAM.
• The Install disk Extended Hardware test does not find a problem.
• Disk utility does not find a problem with the boot drive although a small number of disk permissions always need to be fixed when I run Repair Disk Permissions. Most, but not all of the failed and then repaired permissions are related to Java. One is related to Parental Controls.
• I reinstalled the OS by downloading and executing the Mac OS X 6.5 Combo update.
• I have not installed any new hardware for about a year.
• I am running Disk Warrior right now but it has not completed its check yet
• I have started to use DropBox to protect my User files (mostly Office and pdf files)—get them off the computer, but I am worried about restoring my Applications if I “lose” the system.

Answer 1

Thanks to all of you; I appreciate your expertise and the time you take to help me out. I have made progress. Let me start by saying that my system has 10GB of DRAM memory. One of you commented that I might have needed more disk swap space, but I don't think this is likely. I do think file corruption is a possibility. I am interested in all of your comments but first, will you please explain this in more detail?
"Rebuilding the extensions drivers which are in a cache file, thru Safe Boot, may help - a good driver when installed should force the mkext to rebuild or be deleted, but not all do."
Now, here is the update that I provided to SuperDuper!... In my update I commented that Trash had many more than a million files in it--I think six million. When I deleted the application mentioned below, there is no way that I had that many files, or that much content associated with the app--something pathological happened. My system stability has improved but I will watch for a few more days before I declare victory. In a few days I will do a file system rebuild on the boot drive using DiskWarrior, but I am interested in learning what all of you think might be a better maintenance procedure.
----------------------<snip>----------------------------------
I fixed the problem and SuperDuper successfully ran a full backup.
I bought and ran DiskWarrior which showed that one directory in my .Trash file had about ten sub-directories in it and each one had more than 100,000 files. I think the true number might have been six times that. The directory in Trash was attributed to an application that I deleted recently--SugarSync.
I ran this UNIX command: rm -rf ~/.Trash. It took many hours to complete. When completed I was surprised to see that about 200GB had disappeared from my boot drive--all from Trash and nothing I care about. I ran DiskWarrior again and got a clean report. I repaired disk permissions, re-booted and ran SuperDuper immediately. It copied 249GB in 1:59:00 to an internal drive.
Time Machine now also works.
I think I have some more cleanup to do but I appreciate your help.