Meanwhile, I will see if I can get you a diagram to show you the cable routing you can take with you when you check it.
Print this diagram and take it with you, verify the plug wires go to the correct cylinders
At the dealer level we perform tests in accordance with the symptom. I must take your word on the wires and plugs. You say it was fine before, you know you created a missfire with the crossed wires, If the engine sparks the unburnt fuel in the cylinder at the wrong time and forces a valve shut as it is opening or is burning the fuel with and open valve because the spark is lit at the wrong time, you could cause an internal problem. A simple comparison is all we need to verify combustion chamber integrity. check cylinder 6 and 4, look for a 20% or greater difference. All you need to have to run an engine is fuel, spark, compression and air. the coil shares power from three separte coils inside the coil pack cylinders 1 & 5, 2 & 6, 3 & 4. You do not have a miss on cylinders 1 and 2. this tells me the coil is working. four cylinders have air, because they do not missfire, four cylinders have fuel. You say the plugs have spark. Put all this together it leaves the fuel injectors and compression. Odds on two injectors going out at the same time, very uncommon. What do we have left? Compression.
The miss is on 5&6, sorry I keep saying 4&5, the test said miss between 5&6. I can check the compression tomorrow afternoon. Does this model have an ignition module like the earlier rangers?
The spark is controlled by the pcm. I have attached the workshop manual ignition system overview for you.