I have a 6 Cylinder EF which when started runs for about 2 minutes as though it had only 5 cylinders or the choke was pulled out to far (if it had one). Once it gets running properly it runs very well except for the occasional miss when stoped at lights.
I tried adjusting the base idle speed as per handbook but then it would not idle at all and I have to screw in the idle screw until it would idle.
Any ideas?

have you cleaned out the ISC (idel speed controller?)

read http://www.fordmods.com/forums/documents.php?doc=23

its the second description

yes, pull your spark plugs out and check for signs of water/rust on the plugs ends, mine had same trouble as yours and my head gaskets gone leaking water into the combustion chamber

Replace your plugs and leads while your at it.

If its still there, get your Injectors cleaned.

Maybe doing a diagnostic on the ECU and see what it says. Maybe your HEGO sensor is on the way out.

Also, check for a leaking inlet manifold gasket.

Mine had this problem when I first got it.