OK...so... first off, Ford vehicles do idle fairly fast when the engine is cold. All of mine do this. Both of my Rangers will idle around 1500 RPM and my F150 idles around 1300, until they warm up. Idle speed should drop dramatically when this occurs. I believe spec is 850 RPM w/ auto tranny and 800 RPM w/ manual tranny. Since it is December, I wouldn't be surprised if this is what's happening.
If your idle speed doesn't drop, then you've got another problem. In my experience, it could be a bad throttle position sensor, idle air control valve, sticking butterfly valve in the throttle body, or a vacuum leak, presumably between the upper and lower intake manifolds since you took that apart. I would check the last one first. You can do this by spraying carb cleaner all around where the gasket is, and you will know when you find it because your engine will either sputter or rev up.
A vacuum leak sounds likely because of the theory behind it. Because air is entering the engine from places that it shouldn't, the computer compensates for the leaner mixture by adding more fuel, thus producing higher idle speed.
I guess I need more information to help you troubleshoot this further, like exactly what you've done besides taking the upper intake off. A complete list of symptoms you have at this point would be good, too.