It is very common for the connectors to fail. They are not just connectors on HFM DIS ignition, they are resistors and they crap under load because the spring connector is just a friction fit on each of the 3 plugs under the coils.
What compounds the miss is this is a Waste Spark system, meaning the plugs are in SERIES for each coil, firing 2 cylinders . so a misfire can affect 2 cylinder even if just one connector is bad.
Also, make sure you did not use Plats on this engine ..that would be the same results.