I agree with your assumption that the coils and secondary wires are within spec so let's move on.
There's a test on page 242 in the Service Manual titled "Operational Inspection of the Ignition System ( without the pickup coil) and this test should be your next test. it calls for the use of the "Electrotester" and you can perform this test without having this special tool when you understand the basics of the wasted spark ignition system, so I'll explain this first.
Wasted Spark System- A very common ignition system used in many multi cylinder engines since it saves on the cost of ignition system parts. Basically, the ignition coils fire 2 spark plugs simultaneously. One plug is fired on top dead center compression and the second plug is fired on valve overlap. The spark that happens on valve overlap is "wasted" since it's not required. Now, what you need to understand is the flow path of the secondary high voltage through the spark plug wires and the spark plugs. When the voltage in the primary windings in the ignition coils is energized with 9-12 volts, it creates a magnetic field around the primary windings and when the primary voltage is opened, the magnetic field collapses on to both the primary windings and the secondary windings which creates a high voltage output in the secondary windings able to jump and air gap in the spark plug. In a wasted spark system, that voltage runs down one spark plug wire and crosses over the gap in the spark plug to the "ground" of the cylinder head and across the cylinder head to the spark plug associated with second plug of the same coil, and then jumps the air gap of the second spark plug and back up the spark plug wire to complete the circuit. One spark plug fires from the center electrode of the spark plug to the ground electrode of the spark plug and the second spark plug fires from the ground electrode to the center electrode. This is the reason we have now available double iridium or double platinum spark plugs to extend the spark plugs life. You need to understand the statment in bold before continuing testing.
So, how to perform this next test without the "Electrtester" - You can basically follow the test as written in the manual but instead of attaching the secondary leads to the tester, you're going to point the ends of the 2 secondary wire ends of the same ignition coil at each other and space them 8mm apart and then perform the test. This replicates what happens when using the Electrotester. You should see the spark generated by the coil. if you don't see the spark, try moving the ends of the 2 secondary wires closer together down to 5mm apart. 8mm apart would be a healthy spark, 5mm would be a minimum standard spark. By doing the test as described in the manual, you're supplying the primary circuit with voltage and this confirms most of the wiring in the primary and secondary circuits. So, let's see what you find after this test and we'll go from there.
KB