I received a PM from another member (thanks D B) that gave me the name of a company that works with MSD ignitions. I emailed their company with my current issue. They in return asked if I was running the BIG RED wire directly to the "+" battery post. He said that if I am running it thru a fuse from the battery post, then he has seen similar voltage issues.
Guess what? I am running a 40a fuse off of my starter solenoid (this replaced my original fusable link) and this BIG RED wire is connected at that fuse. This is also where my feed line connection is for my battery voltage guage inside of the car that is showing the 13-15v fluctuation. This is the same connection that my parallel bulkhead bypass wire is connected that leads to my ammeter. Both of these gauges are showing the fluctuation and I wired the BIG RED wire to that same connection.
(vendors description of why not to use a fuse: ""feedback produced by how the box draws current from the system, with a fuse inline this causes an oscillating effect that can drive you crazy trying to find"")
He said that it is a big no-no to run this BIG RED wire off of a fuse. I assumed that since the feed line for this fuse was fed from the starter solenoid which is fed from the main post on the battery, that it would have been fine for the MSD. I know that the instructions say to run directly to the battery post, which I did on the initial install. But to make the wiring look a little cleaner, I changed the connection point of this wire to mount at my main 40a breaker. My mistake!!
(But if I remember correctly, I tested the BIG RED wire on the "+" battery clamp and it did not make a difference. This is why I moved the wire back to my 40a fuse because it looked cleaner.)

I am going to stop by the parts store and pickup a battery cable that connects to the side post terminal with a small red wire attached. I will change this connection so the BIG RED wire connects directly to the "+ SIDE POST" on my battery. This way there is nothing else at that positive battery connection except for the MSD BIG RED wire. Then I will start it up and see what happens. With this change plus the new alternator, I sure hope to see a difference with my ammeter and battery voltage. I should be able to test it this weekend.