I believe you reported an issue with an exhaust smell, but I didn't want to re-read the entire thread. If so, I'd be inclined to believe it is dropping a cylinder, still. So I'd check the plug wires next. Ohm them out and compare the two. check the end caps to be sure they are fitting snug and you feel a "click" when seating them on a sparkplug and the coil towers. Check your primary connections to the coil.

As far as the EMM & injectors, which you swap is six of one and half a dozen of the other. I'd probably go back to the original so the engine serial number programmed into the EMM (and on its label) matched up with the engine.