The MSD on/off wire carries so little current it doesn't matter if the ballast resistor is there or not.
You can leave it as is if you want, or put a jumper across it with piggy back terminals. Or you can remove it. Completely up to you.
Here's a diagram of a way to use a relay to interupt as 67Dart273 was describing.
This is from a previous thread about a disconnect with battery in the trunk, but reworked to show an MSD and working ammeter.
View attachment 1715755114
When the key is off, there is no power to the ignition or to the alternator's rotor.
When the master disconnect is open, there is no power to the ignition or the alternator's rotor.
If you want to keep the ammeter in operation, but take the recharging load off of the multiconnector in the bulkhead, then run another wire through a grommet to the ammeter.
View attachment 1715755116
