Maybe it's time for an Erase and Install???

Things were getting a bit sluggish (like 90% speed drop, and beach balls every few minutes) on my main HD (MacHD), so I created a new backup on my external HD (MacBkup).  This is a cloned, bootable copy, created via Carbon Copy Cloner.  Sluggishness was especially prevalent in Safari and Apple Mail, but at some point would effect almost everything.  First noted this after updating to 10.6.7 and Safari 5.0.5.
Some specs:
•  2.4 GHz Intel Core 2 Duo
•  4 GB 1067 MHz DDR3
•  250 GB HD, about 100 GB not used
•  10.6 (or above)
I've tried a number of options, some of which worked for an hour or a few, but it wasn't long before the bad behavior returned. 
First I tried all the basic stuff, like Repair Disk Permissions and Repair Disk in Disk Utility.  Everything gets repaired.  I used Reset Safari in the Safari menu and cleaned up a number of options there (caches, histories, and the like).  Removed Safari extensions and similar, especially those from pre-Safari 5 days.  Did the PRAM. 
Did an Archive and Install of 10.6 on MacHD.  Did Software Update to bring everything up to date.  Worked somewhat well until Safari 5.0.5 was installed.  Sluggishness returned big time.  Did another Archive and Install of 10.6, but no further Software Updates.  No matter.  It's sluggish again. 
Ran quite a few tests using Disk Genius (DG).  Did repair disk and repair disk permissions using DG. Scanned for bad sectors.  Found none.  Did a Defrag. Supposedly never needed but did it anyway.  The MacHD is still sluggish, sometimes even more so than before.  Ran DiskWarrior.  Created a new directory structure, which was only a slight modification from the existing one.  Returned to MacHD, still sluggish.  While doing all these tests on MacHD, MacHD seemed to be responding normally.  No sluggishness.  Only when booting from MacHD would there be a sluggishness problem. 
Booted from MacBkup.  The bootable copy on MacBkup is only 3 days old, so it's > 99% identical to MacHD.  It runs fine.  No sluggishness. 
So here's where I am today...
•  All hardware tests tell me MacHD is fine.
•  MacHD is only sluggish when booted from.  When accessed by utilities on disk or MacBkup, it seems to run fine. 
•  The cloned version, 3 days old and > 99% identical to the one on MacBkup runs fine, so that tells me my software is in good condition. 
•  All other tests run fine, except for small problems that get fixed, like permissions. 
The only two options I can think of is reclone MacBkup back to MacHD.  But the sluggishness was happening before this clone was made, so I don't what that will accomplish.  Or I can Erase and Install, with all the resultant headaches that go with that. 
So all you Mac Gurus.  Any other ideas on this? 

OK, well things are back to normal.  As mentioned above, the backup I had made earlier this week, one that was already displaying problems, seemed to be working relatively normally on disk MacBkup.  So I figured what the heck.  Just copy it back to MacHD and see what happens.  And it's working. 
Anyway, the maintenance (Disk Utility, Drive Genius, DiskWarrior) I did on MacHD obviously did something.  I thought that I would just copy the problems back, but no.  I'm back to 10.6.7 and Safari 5.0.5 (although 5.0.5 definitely seems slower than 5.0.4). 
Just another reason to keep not only a backup, but a bootable one.  

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