Losing switched power and other #$%&^# electrical issues. HELP!

Okay, the yellow and brown have power only during cranking. No key on power. The brown wire was cut of my factory harness and wasn't being used. I ran a wire from the MSD box to the yellow wire and the car started but the starter drive remained engaged the entire time it ran. If I run the wire to the brown wire, the car starts and will also shut off with the key. One problem solved. However, I an still not charging and show 10.6v at the alternator B+.