Oh wow I feel retarded. I never even noticed there were two sets of I2C pins and was using the two by AREF and GND. Apparently the Due has two I2C interfaces.
Perhaps I should trade my Due back in haha, its obviously too smart for me.
I'll try that library for the MPU-6050 later this evening hopefully and let you all know if my hack job at porting it over was successful at all.
Thanks for your help!