Battery relocation/ NHRA kill switch/MSD 6AL Wiring help needed.

DusterJoe410.4 said
Secondly the blue field wire from the alternator runs to the ballast resistor but we are deleting because the msd box doesn’t need on and will power the coil on its own. So we are trying to trying to decide if we can just delete the ballast resistor or if we should just leave it and delete the coil wire from it and keep the rest the way it was from the factory

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.

DusterJoe410.4 said
The first thing we are trying to figure out is what to do for the alternator kill side of things because the the big wire from alternator wire runs directly to the amp meter and we are still planning to running it for the time being. This is the first time we’ve set a car up with a kill switch so we are in sure of ho to make it all function properly.

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.

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.