If I understand, you still contemplate feeding the alternator to the battery through the small switch terminals. Don't do that.

The whole deal is, (since you have MSD) what you are essentially doing is to wire the small terminals in series with the output of your ignition switch "ignition run" which enables the MSD through the "small red."

By breaking that line with the disconnect, the ignition can NOT "run on" when the disconnect is pulled.

So there is no need to run the alternator clear to the rear, IF you do not use a "Ford" solenoid --just hook the alternator up where the main battery line comes up front.

If you DO want to use a Ford solenoid, you'll just about still need an alternator output line to the battery---and this is my point, I don't see the purpose.