If that's what happened you've sent 5v through a chip on the main PCB backwards, which is never going to end well :(
Theoretically if you find another chip with the same pinout (if you're lucky the model number of the original is written on the chip) and write some firmware that runs on it and find a way to flash it you could remove the dead chip and replace it with the new one, but you don't sound like an expert in all these things so I don't think it's going to happen. I know what needs to be done but am not capable of doing it either...
The good news is you should be able to hijack the existing matrix for both the LEDs and switches and use a Teensy 2.0++ to power them - here's what the back of my Ducky looks like:
Show Image
(http://i.imgur.com/r7OPy3d.jpg)
I don't think there are enough pins to do per LED craziness as you may be used to but you never know until you map it.
The first step for this is to get a multimeter and work out what's attached to what. I've attached a spreadsheet showing the rows and columns for my board with the diode numbers for each key to the left of their ISO-UK legend - if you're lucky it may be the same as your board, but please check as not all Duckys are the same!
Damn, thanks for all the info but that looks way to complicated for me. Guess I'm going to have to use my old rubber dome until I can afford a new keyboard.
Do you think anyone on here would want to buy my Ducky for parts or something?