Tom Kirkman wrote:
You will indeed lose some performance by installing the motor on the side of the kayak, but if you get the motor set right (depth and offset angle) it won't be as bad as you might think. In fact, it'll work pretty well considering the cost difference. You can fabricate your own side mount, a good one, for under $20 and then use whatever your choice in trolling motors might be.
Don't worry about making anything to use as a counterweight on the opposite side. It's not needed. You can easily trim the boat by moving your battery an inch or two off center.
Brian, I had an 16ft old town canoe set up as above and it worked awesome!
I would recommend the Minn Kota Traxxis 45 for motor of choice.