Keyboard, mouse, usb, bluetooth stop working, computer freezes

I have a 2009 MacBook Air. Over the weekend, out of nowhere, the computer froze up where the keyboard and mouse would not work. Plugging in a USB device and/or trying to use a previously paird BT device also failed.
I was, however, able to remotely access the computer since I had previously set it up with LogMeIn. By doing this, the computer had full functionality but external peripherals were not recognized.
Using the remote session, I was able to fire off a backup and send it to a network drive (which was an overnight task, but at least I still have the latest data).
I took it to the apple store and, upon starting it up, all worked fine! We restarted it at the genius bar and the problem occurred again. When the logon screen appeared, the mouse and keyboard were unrespnosive. Restarting holding down any optoin+Key combos did nothing because they keyboard was not being recognized.
Then we restarted again and it worked.
So, basically, the problem is interemittent. They offered the repair depot flat fee cost of $280 that would fix the unit no matter what part(s) had to replaced. It's looking more and more like a logic board issue, but it doesn't make sense that it's only some of the time and others it works fine. So I took it home to try a few more things.
I was able to get it started up using command R and did a full disk erase, followed by a Mountain Lion re-install. I also did a NVRAM reset. That seemed to work for a few minutes, but then it froze up again, although Mountain Lion kept running the install. Once the install finished, I force shut down the unit and started it up again and the keyboard/mouse were working again.
I plugged in an external USB drive, configured bluetooth and started restoring files. It worked for a full day and then the next morning, it happened again. At this point, the keyboard/mouse froze, the bluetooth devices became disconnected and the USB drive dropped - all at the same time.
So, a full reinstall of the OS didn't work (I was somehow hoping this was software related).
Any other thoughts? Should I bite the bullet and just do the flat fee repair?

HI,
Try resetting the SMC, instructions here. http://support.apple.com/kb/HT1543
Try resetting the PRAM/NVRAM, instructions here. http://support.apple.com/kb/HT1379
Try deleting this file. com.apple.bluetooth.plist /Users/YourName/Library/Preferences. Drag that file from the Preferences folder to the Trash, empty the Trash and reboot.
Hopefully something will help.
Carolyn

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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.
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