OK, I will assume that the new controls and new engine harness have the new wire colors. They are pretty standard.
New wiring harnesses have separate battery cables. Positive battery cable connects directly to starter solenoid and negative battery cable connects to lower cowling, on your motor
Smaller engine harness wires:
Red is battery power; connect to the rectifier + post and switchbox red terminal I would jumper it to the positive battery cable as well.
Black is battery negative (ground)(if used). Connect to lower cowling.
Yellow/red is starter solenoid primary. Replaces yellow wire on small terminal of starter solenoid
Yellow/black is choke solenoid. Replaces grey wire on choke solenoid
Grey is tach signal. Replaces brown wire on one of the AC posts of rectifier
Purple is ignition power. Replaces white wire. Connect to white terminal next to red terminal of switchbox.
Black/yellow is ignition killer wire. Unused on your model.
Brown(or tan), brown(or tan)/blue are likely temperature sender wires, unused on your motor
That should do it. Best of luck as you may need to extend some of the wires, or be creative in your routing.
I would connect red wire to solenoid, switchbox or rectifier, wherever it fits best, and make jumper wires to the other destinations. Make sure the jumpers makes good connections.
It would be best to buy a harness designed for an inline six, with ADI ignition, if you can find one with a cannon plug. If not I would get a cannon plug harness for a V6 and hope it can be used without modification.