OK, the only way the engine would run is if you swapped plug leads. I watched the video, more on that in a bit. Swapping powerpacks shouldn’t have affected anything wiring wise, the plugs simply plug in, no individual wires to mess with. The first thing I would do is look at the diagram that was posted, notice the three wire connected that has the orange coil wires. Notice that the number one/top coil orange lead should be connected to the orange lead with the blue tracer coming from the powerpack. If not, perhaps either the powerpack or the coil leads are in the wrong positions on the rubber amphenol connectors. If that looks OK, then I would look at the four wire connector with the brown leads and the black and white leads. Make sure all the colors line up in the connectors.
Yes, changing the powerpack should not have affected any of this. Did you use a new powerpack, or used one? If it was used, perhaps someone had messed with the wiring. Or, perhaps someone had messed with the wiring on your original powerpack. Compare the three pin plugs on both powerpacks to see if the wires are in the same positions.
Finally, the video shows that the engine is spitting lean causing that miss. The first place to start with with basic syncronization. The carb throttle must be completely closed at dead idle speed, and must begin to open at just the right time. There is also that economizer linkage on the side of the engine that might be misadjusted, holding the throttle plan open… Or perhaps the carburetor linkage is damaged holding the throttle plate open. This is where to begin, check your initial low speed needle setting as well.
