Okay, I seem to have gotten my E02 to boot fully into Arch after way too many attempts.
The drives WERE formatted as ext3, but were not syncing properly, or something, and thus getting corrupt regardless.
I used an Arch Linux "live cd" in VMware for making the filesystem and for running e2fsck.
In VMware, I partitioned my flash drive, made the filesystem, then ran e2fsck before installing anything onto the drive, just to be on the safe side. I made sure to safely shut down the live cd before pulling out the flash drive, then inserted it into the pogo.
Once in the pogo, I just ran through the normal installation (starting at "mkdir usb" under /tmp), but instead of "reboot" I did "poweroff", waited for everything to stop, and unplugged the pogo.
Before even trying to boot off of it, I put the flash drive back into the VMware instance and ran e2fsck again. Oddly enough, it did find issues (something about indexes or trees, should have written it down), even though everything had been unmounted and disconnected safely. Told it to fix everything, then ran it again just to be on the safe side. Not sure if it did anything, but I ran "sync" before disconnecting the drive (safely).
I put the flash drive back into the pogo, opened the console, and powered on the pogo. Amazingly, it booted, no issues. Was able to ssh in and run "pacman -Syu" without it locking up or anything. Ran "sync" and "poweroff", power cycled, and it booted back up again fine!
I'm probably rambling, but I'm just glad that it finally booted properly.
And just in case someone needs the syntax for e2fsck:
$this->bbcode_second_pass_code('', 'e2fsck -f /dev/sdX1')
Just replace X with what corresponds to your device, and if it asks if you want to remove damaged indexes/trees (I'll correct that later) just say yes.