Ok once again with a good nights sleep I came in to work fresh and was able to tackle this in minutes.
Basically what had happened is that I was expecting that I would change my model class and a nice new migration cs file would be generated for me. There was no change to make to the model class since EF had auto generated this FK for me originally. I then realized that I could still run add-migration from the package manager console and it would create a new file for me where I could add my own code. I also needed to understand the difference between the Up() and Down() method. Sometimes you take these things for granted when everything is auto generated for you.
Here is what solved my issue:
public override void Up()
{
AlterColumn("dbo.Person", "FavoriteColor_Id", c => c.Int(nullable: true));
}