I have a 1963 Mercury 350 35 hp with 6 pin electrical. It did not come with a controller so I found a used one that has seven pins. There must be something different about the functionality because I keep melting coils and points on one side of the plate. This is the side that has power when I turn the key on. Should there be any power being sent to the coil at that point or should the coil be creating power without sending it 12 volts. The side that works doesnt seem to have any power being sent to it when I power up or turn the motor over? It is running on the one cylinder that doesnt seem to have any power being sent to it?

Thank you

Sounds like you diagnosed your problem already. Until you know the pin out of each do not pass go.

Not my forte but a 5 sec search came up with this...
https://www.outboardparts.com/mercur.../merchrnss.htm