Ok, I tried to upload that code to the uno r3, but unfortunately it doesn't work. It doesn't send anything to the LED (I replaced the Ir Led with a regular one and it didn't flicker). Not sure it you got it to work, but doesn't work for me. Hope it gets figure out, I'm sure making that github code will be useful to people in the future. I'm also going to look into the transistor idea (thanks for the link).
Thanks a lot again for your help man.