If you are certain it's NOT the coils, check the plugs again, then be sure the wires going to the coils are intact and not broken or heat damaged.
It's odd that it improved with the swap, albeit good. One may have not been seated right at least, but since you still have two cylinders misfiring, track it backwards. Perhaps you can score a couple coils from an auto recycler just to be sure its not a coupe bad coils.
Your coils are seating properly, the way you described it is exactly as they are intended to seat.
