Mac Pro Locked Hard Disks

I've been having some serious issues with my new 12 core Mac Pro.  It's a long shot to ask the community for help on this one, but you guys always seem to have the best answers so here goes:
Problem:  Mac Pro has trouble booting (frequently just stops at blank gray screen unless I have install disk in and hold down "D" while booting), and internal & external drives are locked saying I don't have permission to read or write to them. 
History (as best I can remember):  Got the Mac Pro and moved 3 of 4 internal drives from my old MP to the new one.  One sounds like it has a bad drive head and doesn't mount. I replaced the stock RAM with RAM from Crucial.com (24GB of 3 x 8GB as recommended by Crucial, removed all stock RAM first).  Used the computer and started by using Migration assistant in Target disk mode with a FW800.  Although both computers were set not to sleep, it still froze at a certain point in the transfer.  After trying unsuccessfully, I finally did a clean install and went back to migration assistant to transfer only apps and documents (no settings this time).  It stopped during the documents transfer, so I started doing manual transfers from the old computer in Target Disk mode via FW.  I had transferred large amounts of data, and was attempting to open a Photoshop file on the main HD when it gave me a message saying I didn't have permission to open that file.  I noticed the whole folder was locked, so I made the mistake of going to the Macintosh HD (with all system files), changing permissions and applying to enclosed folders.  Obviously, this was bad.  I am not sure if this was before my error or after, but I then saw that all the other internal drives were now locked as were external drives.  After trying several things including booting to Install DVD & running Disk Utility to repair permissions, archive & install OS etc, I was finally unable to boot.  Weird thing is that the same is now true of my original Mac Pro.  I did a clean install of the OS on the main HD of the new MP, and it still wouldn't boot.  I called Apple Support and cut the power, held the power button down for about 10 seconds, held P, R, Opt, & Cmd while booting, and after no luck with that, the guy was going to have me do a diagnostic with the install DVD by holding down "D."  It finally loaded into the welcome to Mac and setup.  I set everything up with the new OS, but am still locked out of internal & external HD's, and still have trouble booting.  I downloaded MemTest and am running in Single User mode and thus far (almost through the 3rd test sequence) it looks like all my RAM is fine.  I'm absolutely pulling my hair out!  Ok, that wasn't really pertinent to the history. 
Does anyone have anything else I should try????
And if you even bothered to read all that. . . THANK YOU!  I really appreciate the guys on these forums. 
Lawrence

And now. . . it seems to boot normally!!!  That's one try after having run the RAM test with MemTest.  I am still locked out of my (non-system) internal drives.  Could anyone just tell me how to use BatChmod to reset them.  I'm about to set owner as my username, but don't know for sure on Group or really any of the other settings.  I've got what I THINK they should be, but I understand I could cause some problems if I'm not sure.  So I'm asking.
Thanks,
Lawrence

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