Went with the Kelly Controls KDS 24v 200Amp motor controller. It comes with plugs and pins to make wiring easy.
I attached it to the inside wall of the hatch under the lip for the best weather protection.
trolling motor fix 008.jpg.
I ordered the weatherproofing option for the controller for $15. The programming allows you to set input voltage on the low and high side for protection of the controller. Also delay on, high throttle bypass, throttle input, speed of throttle acknowledgement, percent of battery voltage output and a few other tricks. The controller wouldn't fit where the factory electrics were so extra wires had to be run from the throttle pot, on-off switch and LED light in the head to the control unit under the deck. Electric taped all the insulated signal wires to the power cable for now. Also incorporated my foot switch on the deck so it really is just like it was from the factory. Bottom line was around $200 from soup to nuts. But it works like a charm, fully variable, with a little dead spot at the beginning of the throttle that I was unable to program out. Decided to go with a little heavier controller after talking with Kelly, this one produces no heat that I could tell. Water test is next. I wanna see if the case ever heats up. The beauty is that the controller is one big heat sink, I doubt it will need any additional mass.