Swap leads on coils and see if spark follows. My money is on the power pack being the problem

Hopefully, bencraschal is correct, always check the grounds/amphenol connections first. Use a good ohm meter that reads low ohm readings clearly. You may want to eliminate the stop switch from the circuit as well, this is done by pushing the stop switch amphenol pin out of the coil 3 pin connector and retesting. You really DO need the expensive amphenol pin tools when working on these systems, please do NOT cut the leads and patch them with butt connectors. Sometimes the pins/sockets get pushed back in the rubber connectors causing a bad/no connection as well. Don’t forget to check the coil primary plug connectors (your motor may not have these), bad/corroded connections here are a big problem that is easily fixed. The spark plug leads are another problem area, the boots/spring clips get rusty/corroded and lose connections to the plug wire.
You can do a little basic troubleshooting by swapping coil connections as well. Let’s just assume that cylinder #1 has no spark and you have checked all grounds/connections/stop switch/leads. Using the amphenol tools, you could swap the coil pins around in the rubber connector. Check for spark again. Now, lets assume that now #1 cylinder fires, but #2 does not. This would indicate that both coils are good, but there is no output to cylinder #1 from the powerpack, you may have a problem with the powerpack/sensor/charge coil. On this engine, there is only one sensor, so it seems unlikely that a sensor problem would affect only one cylinder. But, you could do the same lead swap test with the sensors just to be sure.
It seems unlikely that a bad charge coil would affect just one cylinder on this engine as well. So, in my quick down/dirty test, it seems likely that the powerpack is to blame.
Let’s assume that cylinder #1 still refuses to fire after swapping the coil leads in the rubber connector. Well, this would indicate that the #1 coil/leads are bad.
Let me finish by saying that all components should be completely tested anytime there is an ignition problem and components are replaced. I realize this does not always happen, but it is the best way to be sure that marginal parts/connections don’t eventually damage new components that have been installed.

OK, so your original problem is no spark on cylinder #1/top cylinder, correct? You are saying that you removed the two powerpack orange leads out of the rubber connector, then you put the #2 pack orange powerpack lead into the #1 coil, correct? When you did that, the #1 coil fired, correct? You then tried the #1 pack output lead on both coils, and neither one fired, correct?
If all my statements/assumptions are correct, you most likely have a bad powerpack. Again, be sure to check all grounds, and eliminate the stop circuit from the connector. It is unlikely that the sensor is at fault, but be sure to at least check the sensor coil continuity. The black/white leads in the four wire connector going to the powerpack are the sensor leads. Separate the connector and be sure you are working on the sensor end of the connector (wires leading back under flywheel). The resistance between the sensor leads should be approximately 40 ohms. Now recalibrate the ohm meter to the high scale and check the sensor for shorts to ground. Attach one meter lead to the mag plate, then touch the other lead to either sensor lead. The meter should read infinity, no connection, no shorts to ground.

OK, misread original post…Just edited this post to reflect no spark on #1/top cylinder.

OK, just edited my post to reflect no spark on cylinder #1/top cylinder.