Reverse polarity on Mercury coils

[shortnround]

1994 mercury 135. Have recently changed the rectifier (overcharging) #3 Coil and both switch boxes (new). Still didn't seem to start just right or run good at low RPM. Did more checking and found the coils all have reverse polarity. I did switch the wires on the coils, now the + & - are backwards, but this corrected the polarity, but I'm not sure about running it for any amount of time and maybe damaging the new switch boxes. Any Advice?