WOW!! I ran into a similar or related problem this weekend. I hope you don't mind if I add to this post (I may need to add my own).
Why do trolling motor plugs (both male and female) have 3 wires (or does some equipment use all 3 wires)?, when you only use two of them, one for negative and the other for positive? Black is for the negative terminal, but why is there a blue and a red/orange?
My trolling motor is 24volts, and it only has 2 wire running from the motor. A black wire (for negative terminal on battery) and a "red stripe on black" wire which must be for the positive terminal run in series through two 12 volt batteries.
After having all the real problems worked out on my trolling motor, Minnkota had southwest parts and service replaced the 72lb thrust motor with an 80lb thrust head (now the thing can knock me off the boat if it is pointed either to the left or right and I am not paying attention (preparing to throw the net). I decided to move the trolling motor batteries from starboard battery compartment to inside the cuddy, but I left the previous wiring that runs up to the trolling motor plug on the bow. I purchase 7' of 4 gauge wire from "Boater's World", and solder (followed by liquid tape and shrink tube...the proper way to rig wire that is to be used in saltwater

) this to a new plug, and ran this through and into the cuddy to the batteries. Until Saturday night, I had not been able to get my trolling motor to work, and I thought it could have been the batteries (so I purchased new batteries). It turns out that AlStar Marine wired up everything to use the 12Volt plug.
The instructions from my new ATTWOOD plug indicate that for 24volt, use the blue wire (there is a black, orange, and blue wire). Other than not using liquid tape or shrink tube for waterproofing, I don't know of a problem with this, unless there is a need for the 12volt receptor on the plug. I recall seeing trolling motors indicating 12/24volts maybe it only uses 12 volts during non high demand periods (which might make the batteries last longer). Why would they provide 3 wires. What type of plug is used for 36Volt trolling motors (one with 4 wires??).