Rereading your post, I think I can see why you are having a problem with the coils feed circuit.

So, here is some info to read:

The IGN SW. has 3 Positions ..OFF/RUN/START

When the Sw is in the RUN position, there will be one of those wires you took off from the old system that will have 12 Volts [ battery Voltage] .
That is the IGN wire and that wire goes to the coils Pos+ terminal.
When the key is ON, you have 12v, when the key is OFF, you have no volts..that is the IGN Wire you want to use for the Pert system.

The wires from the starter are only activated when the Ign sw is in the START position ..that is of no concern to you now b/c that is the old Ballast By-pass circuit...where the ballast was by-passed as an aid when you Crank the engine. That is not IGN feed that the Pert system needs ..you need the RUN position 12v , not the Start position feed....

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A Dalton