Given the MAP/MAF/EGR references I assume you have a KJ CRD. When you say it idles rough is it more like the engine is shaking but the rpms at idle stay steady? If so I'd speculate that both your motor mounts are shot. Generally you can tell which one by putting your foot on the brake and seeing whether the vibration is worse in drive or park. Since you say it's bad in both I'm guessing both mounts are bad.
Why, if it's mounts, it would do this only "after warm" I have no clue but rough with brake on and not with brake off does not, to me at least, suggest an engine/fuel/drive line problem.
It's not terribly hard to pull the passenger side motor mount (see
http://www.greendieselengineering.com/f ... t/115.page) to check it. If torn or when shaken the mount sounds like it's full or marbles then the mount is shot. FYI left and right mounts are identical but for the heat shield. You can save about $10 by ordering 2 driver side mounts (52129011AD) and swapping the heat shield from your old passenger side mount to one of the new ones.
Drivers side mount is apparently harder to do but still can be DIY.
Drop me a PM or email if it's mounts or something else.