One wire alternator problem
Have you read the Mad article? That gives a VERY good overview into what you are up against. It takes some reading It's worth it
Try wiggling the bulkhead connector parts while the engine is running/ charging and while you are monitoring the "run" wire voltage there under the hood
By the way your MSD "big red" should NOT be hooked to that, if it is so now. The "big red" should be hooked direct to a battery source such as the starter relay stud
The "small red" is a "trigger" wire and should be hooked to the old "run" wire. Now that the ignition is not running directly of the blue "run" wire, there should be very little load on that wire. There is no longer an ignition, nor an alternator field / regulator circuit.
Do you have an electric choke? Check that out for shorts, etc.
What smog equipment is still hooked up under there?
Also, while running / and monitoring the blue wire, "wiggle" the key a bit.
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One last thing.............what is the routing of your cables which supply battery to the starter relay?
Your main big battery cable goes from the battery to "where?"
What jumpers over to the starter relay?