Lion Stopped Seeing External Drives

I've been running Lion on a 2.8 GHz, i7 13" MBP I bought new in January. When I got it, I partitioned the 750 GB hard drive into two drives so that I could create a second bootable Admin partition from which I could run repair and diagnostic software on my Main drive. (I run my computer pretty hard. Even sleep with it next to me. But that's another story....) Both partitions are running the latest version of Lion with all updates. I tend to mess very little with Terminal tweaks. And all of my software is either from a) A very well-known dev company, b) the Mac App store, or c) Rated very high with lots of reviews on MacUpdate. I run Virus Barrier, LittleSnitch, DriveGenius / Drive Pulse to help ensure everything is running fine. I have 50+GB of free space on my Main partition.
Yesterday, I was transferring data from one external 4TB G-Technologies RAID drive to another identical drive — daisy chaned over firewire 800. After copying the first 2TB, I kept getting Finder crashes after every few hundred GBs were transferred. Had to reboot after each crash because relaunching the finder would shut it down, but not bring it back up. Finally, after one of the crashes, the Main Lion partition I was working from stopped recognizing the external hard drives, except for in Disk Utility.
I booted to the Admin partition. That partition recognized the drives just fine. I ran every diagnostic possible on the Main partition. It checked out completely fine. Booted back to the Main partition. Still no ability to recognize the drives. Ran Lion recovery on the Main drive. Then ran all the re-needed software updates. Still no ability to recognize external drives. I haven't attempted to repair the external drives, since they are fully readable from the other partition.
Any ideas what might be going on? My next step is to copy the contents of my Main partition to an External drive from the Admin partition and then wipe and do a clean install of Lion on the Main partition. I'd much prefer to just be able to do a clean install of Lion without wiping my drive or data — the way we used to be able to do reinstalls back in the day. But I don't have that option from the cloud installation and I can't find any articles to see if that option would be available if I were to create a bootable USB of lion. I'd like to not spend the money on a Lion download if it won't be able to do this kind of system reinstall for me. If it can, I'm thinking my problem will be solved....
Has anyone tried this kind of reinstall from a bootable Lion USB? Does it work? Help....

Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of this exercise is to determine whether the problem is caused by third-party system modifications that load automatically at startup or login. Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards. Boot in safe mode* and log in to the account with the problem. The instructions provided by Apple are as follows:
Be sure your Mac is shut down.
Press the power button.
Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone, but not before the tone.
Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear).
*Note: If FileVault is enabled under Mac OS X 10.7 or later, or if a firmware password is set, you can’t boot in safe mode.
Safe mode is much slower to boot and run than normal, and some things won’t work at all, including wireless networking on certain Macs.
The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.
Test while in safe mode. Same problem(s)?
After testing, reboot as usual (i.e., not in safe mode) and verify that you still have the problem. Post the results of the test.

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Message was edited by: John Galt

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