Justin - glad to hear that you are having some success. I am like you, with the MG Digital Tour. I checked to see if there was any resistance between the starter battery and the trolling batteries, thinking that if it was none, then the charger would not effect me. Did you ohm out between the two battery systems before you disconnected the on board charger? I've heard of people installing a switch between the on board charger and main starter battery.
I have the ferrite magnets installed on the transducer and power wires to my Garmin unit. They made no difference to mine. I will try disconnecting the battery charger next. I've run out of options at this point. I did install some foam between the transducer and transducer clamp with no change this past weekend. When I turn my unit on, I have to adjust the gain manually down to less than 50%, and pending on the speed setting of my trolling motor, sometimes even less. It sucks!