Sorry to dig up this old thread of mine, but I finally got time to do the LIM job and solved my problem, and so I wanted to check in and explain for anyone who might read this in future with the same problem.
To recap, I had idle misfires, most but not all in cyl 4 - and only at idle. I also had very negative fuel trims - only at idle - and, though I didn't mention this in the original post because I didn't realize it might be related, I had hard starting (3-4 seconds) EXCEPT when cold.
These hints come together to suggest leaky fuel injectors.
When I did the LIM job, the gasket was in great shape, as was EGR tube, and vac did not change after the job - been 19-21 inHg the whole time. That nice high vacuum combined with negative fuel trims means I don't suspect vac issues.
However, sure enough, I installed reman flow-matched injectors from ZZP (much cheaper than new) and ALL the problems are gone! No more negative trims, fuel pressure holds so car starts instantly, and best of all, no more idle misfires, even at long, hot idle! See Torque screencap below...
So if your symptoms seem to match mine, consider that it may be leaky injectors.
One way to test that doesn't involve removing injectors is simply to check the fuel pressure after the car hasn't been used for a while. If it's zero, you may have leaky injectors like I did! You can use a proper fuel pressure gage, or just push in the valve stem carefully on the fuel rail and see whether fuel sprays out at high pressure. Mine did not just a few hours after ignition off, indicating pressure loss from leaky injectors (note: other things could cause this too. I replaced the fuel pressure regulator in the past to no avail...)
Perhaps you could fix the leak just by cleaning the existing injectors, idk. I went with remans to be safe.
Hope this helps someone!
Thanks,
Komrad36