I think it's pretty clear the phone isn't on 1.3.1, so it's never mounting the internal storage as a USB drive.
My Pre on Win7 does the same thing when I plug it in for just charging, shows a drive that needs a disk inserted.
Anyway, from what I hear, the new webOS Doctor for 1.3.1 doesn't erase the media storage partition. I'd wait for a second opinion from someone who has used it though.
It sounds like what should work (though again, I'd wait for confirmation) is the following.
Turn off your broken Pre, and hold the volume up button while plugging it in to get the huge USB logo you mentioned.
Run webOS Doctor for 1.3.1 which will upgrade to 1.3.1.
Then, half an hour or so later or whatever, when the broken Pre has finished updating, you should be able to plug into the USB port, and then that Sym + Orange + U shortcut that's been mentioned a few times here will switch from "Just Charge" mode to "USB Drive" mode.