I believe there are some apps and I guess multi-player games that require you must use a controller in port 1. However i've just tested this with a a Duke controller and two official Controllers S types on their own in various port position combinations and all worked perfectly when navigating the UnleashX dash.
you can usually just use a USB cable, you have to swap white and green IIRC. other than that, it's the same cable
If it is one of the wires inside the controller broken there shouldn't be any need to replace the whole cable but if it is not just that then replacing the whole of it with a USB one is a good idea as long as you wire it up correctly.
If it's an official XBOX controller, the wire colors and functions in the cable are the same as USB, just ignore the yellow one in the XBOX cable as it's not used, no swapping of any colors is necessary.
Nope, color, function and even the pinout is all but the same as USB.