Well, whenever I get on one of these discussions you never know what level of expertise one has. You obviously have enough to run "top" etc. which puts you leaps and bounds above other (that's a compliment! :-) )
Based on what you've said, I suspect you have a drive problem. If you've downloaded SCSC's book on hard drive troubleshooting, take a look at the sections on errors, irregularities, and scatter. Errors are bonafide failures in disk access and they ALWAYS generate an I/O error. Irregularities (Scannerz is the only product I know of that can detect them, in the world of Windoze they like to call them "brown sectors") are problematic sectors which read slowly but are readable for whatever reason. Scatter means the problems are inconsistent from test to test. A bonafide platter surface problem will have no scatter, the results will be repeatable from test to test. Problems caused by intermittent failures (SCSC's book calls these "generic failures" which are due to cracked traces, faulty solder joints, etc) will display scatter - problems will appear but they're RARELY repeatable. Probably the most famous (or infamous) example of a generic failure is the separation of the piggy back ball grid array video chip used on iBook G3 w/CPU frequencies of 600MHz - 900MHz. Another example is the failure of some RAM slots on 15" PowerBook G4s, but this wasn't widespread.
With all that said, irregularities are problematic because most drive tools fail to acknowledge them. If a sector is deemed "readable" even though it may be taking seconds to read it, it's still deemed a good sector. Drive's have to compensate for the fact that there's multi-tasking going on, and in some cases some events may take a second or two to become noticeable. The problem comes when the file needs to be read tons of times (like a cache file for an application). Suddenly, a 1 second delay, if it needs to be accessed, say 100 times, becomes a 100 second delay.
If you lived in the U.S. I would probably encourage you to just fork over the 30 or 40 bucks that Scannerz costs and use it, but there may be some type of import/export restrictions on something like that (in other words, they may not be able to sell it to you...I'm not an export attorney but I've heard of such things happening with other products - especially the cutting edge type stuff). Additionally, if you've downloaded their manual, and let's be real, it's not exactly written for an audience elementary school music teachers (PLEASE don't tell me you're an elementary school music teacher! :-) ) it's obviously been written for service people, IMHO.
Instead, what you might want to try is this, and it won't cost you money, but you will need admin access:
1. Open up terminal.app from the Utilities folder - you already know how to do this, I think.
2. Type in "cd /var/log" but you may need to type in "sudo cd /var/log" - you'll likely need admin privileges.
3. Type in the following command exactly as it's written:
grep "I/O error" *
What that does is tell all log files (*) to report occurrences of the string "I/O error". If there are I/O errors they'll likely identify either an entire disk (like disk0) or a volume (like disk1s2). If it's a volume, use Disk Utility to identify it. If no I/O errors exist, I would assume that there's either a software compatibilty problem of some sort or you've got irregularities.
One of the things I've found interesting is that SCSC typically releases a version of software for Scannerz within weeks of the release of any major OS version updates, but looking at their logos for Scannerz and FSE, they're STILL not saying "Mountain Lion Compatible." Maybe they're slow, or maybe they know something the rest of us don't.
You might also want to check other posts on this site to see if others are having similar problems with Mountain Lion.
I certainly hope this helps you out, and good luck.
