How to identify damaged files in ext HDD?

Early 2008 iMac - iMac8,1 - Intel Core 2 Duo - OS X 10.6.8 - (int) Samsung SSD 840 EVO 500GB - (ext) OWC Qx2 enclosure w. 4x2TB TOSHIBA DT01ACA200 - Wacom Intuos Pen&Touch tablet (no mouse) - DSL - Flash Player.
I think hardware is the place for this question.
I inherited this iMac back in May/June, spent a month or two with it, did a fresh install of Leopard, and then Snow Leopard on top of that. Everything seemed fine. Speedy response. Decent browsing speed, even with my crappy 3 Mbps DSL.
I added two separate HW upgrades: a SSD int hard drive + RAM to 4GB (installed by reputable local shop), and added a 4-bay ext HDD set up as 4 independent drives, JBOD (purchased from OWC). I feel I made a mistake in doing both of those things at the same time, as I immediately encountered glitches that have been hard to troubleshoot. The worst was the ext HDD / enclosure suddenly un-mounting all by itself, complete with error message ("was not ejected properly"), promptly after which the drives reappear on the desktop, with their contents seemingly in place.
I'm not looking for help troubleshooting; I think I've found the problem, at least for the un-mount issue (bad FW port, thankfully there are two). There might or might not be lingering stall-when-opening-folder issues, too soon to tell. Both vendors have been helpful with their responses.
What I'd like to know is how (or if) the contents of the ext HDDs can be scrutinized for damage? This un-mount thing happened at least a dozen times, and several other times I was forced to manually shut down the HDD enclosure when everything else was frozen. I have to think something's been corrupted or damaged with all of that un-ejected off-and-on activity.
Any input is appreciated. Thanks in advance!

Old Toad wrote:
Have you run any cleaning or optimizing apps like MacKeeper or CleanMyMac?  Those are known to cause serious problem with Macs including slowdowns,
No, I've always avoided those like the plague. The pop-up ads for that crap are the obvious cues to stay away!
Linc Davis wrote:
The only meaningful test of whether there are "corrupt files" is to use the computer. If it behaves normally, you can assume that the operating system and applications are intact. As for your other files, open the most important of them and see whether the contents are what you expect.
Though swapping the FW port SEEMS to have stopped the sudden un-mounting (maybe not enough time spent scrutinizing that yet), there is still problematic behavior. Just this evening, after the desktop was on all day but saw little use (Safari, iTunes), I tried simply opening one of the hard drives:
- 8 minutes to simply open the window. Spinning beach ball. Window changed dimensions from prior use, appeared as though it was opened for the first time. It showed no contents.
- 20 more minutes to show contents. During this time, the spinning progress wheel spun. Contents finally showed up.
- 8 more minutes to open one folder. Spinning progress wheel.
Contents appear to be there. This is a storage disc, no backups ever performed. This new 2TB drive contains only 100GB.
This stall seemingly caused other stalls elsewhere. Namely, a simple text copy-and-paste function in TextEdit. When the HDD finally decided to finish, TextEdit was available to me again.
Welcome to my world.

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      DATA: lwa_errormsg  TYPE iwerrormsg.
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      DATA: lt_conn       TYPE STANDARD TABLE OF bdn_con.
      DATA: lt_conn_tmp   TYPE STANDARD TABLE OF bdn_con.
      DATA: lt_objcont    TYPE STANDARD TABLE OF soli.
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      CONSTANTS: lc_period(1)    TYPE c              VALUE '.'.
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              filename                  = lv_fullpath
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    *          HEADER                    = '00'
    *          TRUNC_TRAILING_BLANKS     = SPACE
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    *          COL_SELECT_MASK           = SPACE
    *          DAT_MODE                  = SPACE
    *          CONFIRM_OVERWRITE         = SPACE
    *          NO_AUTH_CHECK             = SPACE
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    *          FILELENGTH                =
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              data_tab                  = lt_objcont
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              file_write_error          = 1
              no_batch                  = 2
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              invalid_type              = 4
              no_authority              = 5
              unknown_error             = 6
              header_not_allowed        = 7
              separator_not_allowed     = 8
              filesize_not_allowed      = 9
              header_too_long           = 10
              dp_error_create           = 11
              dp_error_send             = 12
              dp_error_write            = 13
              unknown_dp_error          = 14
              access_denied             = 15
              dp_out_of_memory          = 16
              disk_full                 = 17
              dp_timeout                = 18
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              dataprovider_exception    = 20
              control_flush_error       = 21
              not_supported_by_gui      = 22
              error_no_gui              = 23
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    * MESSAGE ID SY-MSGID TYPE SY-MSGTY NUMBER SY-MSGNO
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    *          file_open_error       = 1
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    Last September, there was an invalid reference in the metadata and I had to fix that invalid
    reference in order for fsck to not return an error. Since this damaged file was modified
    around the same time, I am guessing that this is the file that was damaged as a result
    of fixing the invalid reference.
    Can anyone identify what file this is and how I can replace it?
    -Chris

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