How do the spark plugs look? With the engine running so badly with the many things done, I wonder how they are now. If any of the plugs look rough, wet or black etc, there may be something wrong with the gaps, coil packs, or the plug wires themselves. The plug wires are easy to damage when pulling them off, old or new.
If one or a few of the plugs look bad, you may have to replace them, or the wires, or all of them, depending on how they are. I'd pull the plugs and carefully inspect each one, and the wires, documenting the condition, don't mix them up, and consider why any would be fouled etc.