Two things come to mind right off for me...
-I had a similar problem with mine when I first bought it and it turned out to be a broken valve spring. You may want to pull the valve cover and just have a look.
-The ECU's VERY rarely ever go bad in these trucks, but when they do it's typically in the injector circuit and it effects the #4 injector. Try unplugging the injectors one by one while it's running and see if you find one that does NOT make or make little difference in the idle. I know you said you had the injectors cleaned professionally, but were they flow tested as well when cleaned to be sure that they are actually operating properly?