Great Job in thorough detective work.

If you have a smooth idle now, with it lean, that means EVERYTHING is right on. It has to be or it will not run smooth. Intake leaks are not uncommon around th efuel injector seals, but since yours are new--should be 4-5 years before you have that problem again. Now run good fuel to keep the injectors and intake valves clean. That has a tremendous impact on idle quality. Even a little crud on the intake valves will cause a rough idle, especially at start-up.

Often you can improe idle quality and emissions level by increasing the spark-plug gap. It takes more energy to fire a lean mixture and a wider plug gap will help there. Of course plugs have to be sharp--not rounded off edges. You might get a miss at high speeds and loads if the gap is too wide for your coil and wire condition..