Flickering Lights

Went out to the garage this afternoon to take a look at the wires running from alternator to VR and other wires as I had problems with wires in forward light harness. Thought I might find something wrong with the engine wiring harness.
Well this is what I found after unwrapping the wires:
1. Two wires from one field post on alternator going to VR post I.
2. One wire from other field post on alternator going to VR post F.
3. Yellow wire attached to field post on alternator connected to black wire that is then connected to green wire which then connects to VR post F.
4. Black wire attached to other field post on alternator and goes to VR post I. This wire is connected to blue wire and these two wires are then connected to white wire of VR plug. Blue wire goes to alternator, but was cut about six inches back from the alternator. Presume the black wire was run to replace the blue wire, but do not know why.
5. Squeeze type unions used to join wires. Plastic on one union was melted.
6. Alternator is a squareback. Both field terminals are insulated.
Shouldn't blue field wire be "Td" into the on side of the ignition switch? Was looking at a wiring diagram and green wire was going from one alternator field terminal straight to the VR F post. Blue wire went from other alternator field terminal to the VR I post but there was also a blue wire that was "Td" into this blue wire that went to ignition side of the ballast resistor.
I guess that I need to make this connection to the ballast resistor, or can/should I make connection somewhere else?
What harm was caused by this type of connection between alternator and VR?