We got a response from customer service and it seems to have fixed our issue! Also our prints are infinitely better than before the problem occurred (funny, because we just assumed the myriad of minor issues was a common occurrence such as bad infill, top layers not filling, slopes drooping/not printing, etc... ).
So, for future visitors that might have the same problem - our issue was the cord (red) going to the y-axis motor was pinched behind the feeder motor. After freeing it, we've had great results with our prints.
Also, again thank you for the responses gr5.