Bronzer, I tried, unsuccessfully, to see if your trolling motor was a variable digital controlled (Digitizer or PWM) TM or not. But I can't get a good review or info whether it is or not. If it is merely a preset speed control system, then you may need new brushes in the TM. If it is a PWM digital design, then that circuit can interfere with other electronic accessories on board.
You can install some filter networks on the other power lines that power the locators and that may help, unless the noise is EMF generated by the motor. If it is that type noise, it is going to be a lot harder to fix. Since you stated that the TM is running on its own battery setup, then it is looking more like EMF noise and not following the power lines back. Are the grounds from each battery connected together? The noise can travel that connection as well.
I would be looking more at the motor in the foot section for the possible noise source and service that foot with new brushes, bearings and seals. But without being there and doing some tests myself, that is merely a wild guess. JMHO