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I can't tell you for sure, but by means of deduction I'd say that the wire from the ignition switch must only be hot with the key on (run), and the wire coming form the solenoid must be to provide voltage during cranking (because the first wire must not during cranking, only in run).
If you're installing a MSD-6A then you'll want to remove them both. You can test my theory with a test light, and if that's the case then you can probably splice them together and run them to the small red wire on the MSD box, unless you've already identified another "key on only" source.
Hope that helps if no-one else has more specific info.
The wire from the ignition is a resistor wire. It is supposed to be about a 9 volt wire to the coil. The wire from the selonoid is there to boost the voltage to 12 volts to give it an extra "jolt" to get the car started. If the 12 volts is there during running it will burn the points up and get short point life. The MSD unit needs 12 volts. I would tape these off and find a good 12 volt source and run that wire. I must have missed your post in the C3 section. Hope this helps. I have a Crane HI6 which is wired the same way as MSD units.
jack,
If I am reading you correct there is an insulator there (on the coil) and if I remember correctly I hooked both those wires to the coil on a Camaro racer I had once and BURNED UP A NEW BOX!! ...redvetracr
PS Hit the MSD website, I think they have all the possible wiring diagrams shown