MSD/Starting/Charging Issue, Novice Needs Help

Hey FABO members, you have helped me greatly in the past so here I am again.

The short of it:
A. system not charging, new VR
B. starter cranking like the timing is too far advanced, but it isnt!
C. MSD question regarding 12v to my distributor per diagram supplied by MSD.
It shows switched 12v going to my Mallory Unilite Distributor, the problem is that when you crank it to start the engine the 12v to the distributor is gone, its now in the brown wire (start circuit, old coil wire)....and the car wont start.
When I add the brown wire to the circuit it fires up but the volt meter reads about 10v and the car is running rough.
Something just doesn't seem right.

Can you guys take a look at this diagram of my system and see if you can tell whats wrong. The drawing is showing the brown wire not tied in, as shown, the car will not run. If I take that brown wire (old coil) and tie it to the blue(start) the car will run but its running rough.

Does it look like the VR is wired right?

Any help is greatly appreciated.
Greg