I have a modified Colorado with a higher mounted seat and standing panel where the normal footrests would be along with a bow trolling motor mount. The first couple of times out, I've found that the changes direction on its own quite a bit, requiring me to stay on the trolling motor to correct it. It also never tracks straight with the trolling motor straight.

 

I think a fixed rudder would solve the hunting problem. Has anyone does that mod before on one of these boats? I'm curious about proper sizing and how strong a shaft I really need.

I don't have that boat, but I can tell you that your conclusion is correct.  On my old town kayak with front mounted trolling motor you can be moving 'straight' and the back end will kick out significantly (even more if there is a tail wind or current) if you don't have the rudder down.

 

I've seen DIY versions on other boats made from plywood that is 6x12".  Mount that to a piece of angle iron or anything else that you can readily mount to the back of your pontoon.

When I was in Colorado, I saw them built out of pvc and plexiglass- the actual rudder was about the size of a shoebox lid. I also saw people that just zip-tied a rudder to their trolling motor shaft above the motor, so that may be an option as well. The wind out there is no joke.

I'd add a skeg off of the back. It will keep you from "wind vaning".  Not sure how long your Colorado pontoon is.  But I made one for my kayak out of 3/8" nylon cutting board. Also you might want to make it so you can raise it up when you want the maneuverability or when you beach the boat.

FM

 

Several adjustable rudders available on the market under $30.

Tom