Anyway, regarding the subject..
First thing you'd have to decide is how to shorten up the shaft of the trolling motor.. Maybe even do away with it all together? As I mentioned to you before, I've seen real fancy kayaks the have the trolling motor attached/recessed into the bottom, complete with hand controls and foot peddles for the rudder! It looked kewl and all, but you'd destroy it in these ozarks rivers pretty quick just because there was no protection for the motor...
Second is handling.. Are you planning to steer with the trolling motor, or ruddering with your paddle?
Battery weight will always be a problem, but as someone pointed out you could just re-purpose a small battery from a smaller car (salvage yard), they weight allot less and would prolly still do the job... You'll definitely need to consider counter weighting your battery on the front end of the boat, or maybe you could run wiring to the front of the boat and put your battery there? (guess that depends upon the structure of your boat, eh?)