So just an update on this. I took the motor apart (not the easiest of tasks, the power connectors are soldered onto the brush plate connections, and you need to get these off to pull the casing out. I ended up having to cut the connectors on the wires.
So pulling it apart, there were no signs of any water getting in and the brushes were clean as a whistle. The only thing that was in bad shape were the 2 seals. So this leads me to think that my original hunch that the issue is the main board going bad.
So ordered a brush kit (seeing that I have it opened, I might as well do some maintenance) and a main board from Northland Marine (
http://www.northlandmarine.com), great guys! responded to my emails promptly and helped out with all my questions! Check them out for all minnkota parts and great service!
Received the main board, hooked it up, comes with all the heat shrink for all the connections and wiring instructions (triple check these) you don't want to have to order another main board!!!
Replaced the seals, they were corroded really bad, needed to smash them out with a chisel and hammer. Glad I ordered the flange bearing too, because I kinda ruined the old one when I was trying to get the seals out. Placed the seals in, put the new flange bearing in. Replaced the brush plate, connected it all up.
Plugged it in, fingers crossed! started it up and it is all working, speeds 1/2 through to 10 working again! pretty stoked!
Let me know if anyone would like to know more details about any of the steps.