If you need to stick with your existing unit, most of the minnkotas are bushed motor, with a potted controller in the head, and two power wires going down the shaft. You could hack that and add a more powerful controller, but waterproofing will be important, esp if you want it to run after a capsize recovery. If you go that route, you could also mount the controller in the boat, with just the power wires running to the motor with the shaft caulked tight.
Have you checked your existing motor for water intrusion? I've serviced several of these that ran, but with bad power, where the lower unit was full of water. It can get in around the prop shaft seal, even when the top is fully waterproofed.