Just for the sake of a little review, lets take a look at the procedure to make sure we are both on the same page...
Setting the base idle speed:
First of all, the idle needs to be adjusted to where the speed is at or below 600 RPM with the IAC disconnected. If you have a wild cam, you may have to raise this figure 100-150 RPM or so. Then the electrical signal through the IAC can vary the airflow through it under computer control. Remember that the IAC can only add air to increase the base idle speed set by the mechanical adjustment. The 600 RPM base idle speed is what you have after the mechanical adjustment. The IAC increases that speed by supplying more air under computer control to raise the RPM’s to 650-725 RPM’s. This figure will increase if you have a wild cam, and may end up between 800-950 RPM
Remember that changing the mechanical idle speed adjustment changes the TPS setting too.
This isn't the method Ford uses, but it does work. Do not attempt to set the idle speed until you have fixed all the codes and are sure that there are no vacuum leaks.
Disconnect the battery negative terminal and turn the headlights on. Leave the battery negative terminal disconnected for 5 minutes or so. Then turn the headlights off and reconnect the battery. This erases the computer settings that may affect idle performance.
Warm the engine up to operating temperature, place the transmission in neutral, and set the parking brake. Turn off lights, A/C, all unnecessary electrical loads. Disconnect the IAC electrical connector. Remove the SPOUT plug. This will lock the ignition timing so that the computer won't change the spark advance, which changes the idle speed. Note the engine RPM: use the mechanical adjustment screw under the throttle body to raise or lower the RPM until you get the 600 RPM mark +/- 25 RPM. A wild cam may make it necessary to increase the 600 RPM figure to 700 RPM or possibly a little more to get a stable idle speed.
Is this the procedure you were using to set the base idle speed?