kalera
Okay everyone, I was able to switch the connectors and now everything is working fine. Thank you Repetier for pointing me in the right direction.
If anyone is experiencing the same problem; I fixed it by opening the file "pins.h" and replacing all the values of "ORIG_E1" with the values of "ORIG_E0" and vice versa. I did this for all of the Mega boards since I wasn't sure wich board Felix was using.