UPDATE:
Progress! I finally got access to an xp computer. got ide installed and the libusb0.dll driver for the MKII. It did exactly the same thing as with AVR studio. I wrote a simple blink code and wha-do-ya-know...it worked!
At this point I have determined that there is a problem somehow with the lcd screen. I checked that all my pin assignments are correct. It will initialize with no problem and give me a cursor. I can even move that cursor anywhere I want. I can turn the back light on and off. However when I try to print to it, it does essentially nothing. If I tell it to print any single character (that I've tried) it prints a bunch of spaces followed by "45" followed by more spaces. It's late, I have to go to bed. but if anyone has ideas as to what the problem might be, please let me know, thanks! Goodnight world.