I experienced a situation situation similar to what you are dealing with here. Back in the early 80's my dad bought an early 70's van. It had a 360 in it and the tranny was bad. Dad put a tranny that was mated to a 318 in it. That motor always had a vibration in it like it had a dead cylinder but when you would pull the wires off one at a time they all would drop rpm about the same. This went on for over a year trying to find this " miss " in the engine. Next my grandfathers 318 in his pickup was getting tired and he had a low mile 360 out of a car to replace it. I went to this mopar guy in search of a pickup oil pan and pick up tube for the 360. He told me to make sure I change the torque converter because of the external balance of the 360. As soon as he said that I new what was wrong with dads van. We changed the converter in the van to a external balance and it ran smooth as silk.