You got some problems there baybreaker . The most obvious thing that you got going on is the 120 v ac feeding the battery charger is back feeding somehow to the negative side of your electrical system . Normally I would say that since it is your trolling motor battery charger it should be isolated from your starting battery in turn isolated from the motor which is "grounded" to the negative . It is soumding like it might be bonded somewhere possibly a ground or negative bus bar. Since you are touching the motor barefooted you are compleating the circuit which in turn could be for starters you lost a nuetral somewhere and it is looking for an easier path to ground , that would be you . Or it is shorted out somewhere , this is vague that's why it's a starting point , and you're getting ac where it should'nt be , obviously .
What you're gonna have to do is start check everything from the source , like a river . I would start with extension cord . Make sure it looks good , if has a factory end good . If it has one of those replacements ends make sure it is put on right . After that trace out the wires that come from the male plug that goes through the console back to the charger . Make sure everything looks good , isolate the secondary side ( the wires going to the batteries ) check the voltage coming off them , check for a/c , d/c and polarity . If you have any ac voltage on the secondary side the charger is shot more than likely .The diodes in the full wave rectifier no good
This should get ya going emial if need email@example.com