Here is a diagram of the CDI ignition:
http://kawatriple.com/cdih2/cdih2.jpg-The hi/lo spd coils feed a signal thru individual channels to charge a capacitor.
-The pickup generates a pulse to trigger an SCR that releases the energy stored in the capacitor.
-The released voltage charges the ignition coil that produces spark.
A weak pulse from the pickup may intermittently fire the SCR.
The SCR should fire with a certain amplitude pulse.... age may change the trigger point of the SCR.
The capacitor can become "leaky" and not hold a charge due to aging.
The effect of all of the above can be affected by rpm.
This is a simplified explanation to show that there are several components within the CDI that can make spark weak or marginal due to aging of 40yr old components.
IF the pickups measure ohms proper and the air gap is correct, the ignition coil has been swapped with no change, I'd recommend getting an "all in one" box from Lakeland.
http://www.lakeserv.net/kaw/h2_all_in_one/index.html