We need a few more details.
Does the bot make startup sounds when you turn it on (play the MakerBot song)?
Understand that there are actually 2 processors in the bot. The first one is the 8u2 that the USB port is plugged into. If you see that when you connect to a computer the bot shows up, that means the 8u2 is working. But all that chip does is creates a USB to COM port (remember old serial ports on computers before USB?).
The main processor that actually runs the bot and controls the LCD is an atmega1280.
What happens is that maybe someone tried to update the 1280 and messed it up with bad code or a bad sequence.
The problem is, there is a tiny bit of code called a bootloader. Normally, chips can ONLY be programmed with a special programmer device. The bootloader code starts the instant the chip is turned on and would allow for programming without a programmer over the USB to serial communications path.
So likely, not only do you have non-working code on the bot, but you also likely have corrupted with bootloader and therefore cannot flash via the normal update process.
Further, MakerBot support didn't help you out. They gave you a tool for the newer series of mainboards in the Replicator 2 series of bots. That tool cannot fix your problem if the bootloader is corrupt.
But, let's also be realistic here. The Replicator 1 is KNOWN to blow up the electronics. You have a suspect situation. The best thing you could do long term is to send that board to one of us to perform the procedure and replace the regulator known to kill the board.
Heck I'll do it for free, but you either have to send me the bot or send me the board. I'm all for keeping these old machines alive as I think they are better than the new machines if you fix this problem.
As you can see, they are all of $5 for a lot of peace of mind.
Alternatively, maybe a member of the group is near you and can help.