1994 Ford F-150 WONT PASS SMOG

Check engine light on?

Two things to check first. The coolant temp sensor may be bad. When they go bad, the computer that's reading the info coming from them sees the engine as never reaching operating temp, so it keeps the cold idle and mixture settings.
The IAC motor may need to be cleaned as well. It's the tubular looking thing alongside the throttle body. Blasting the inside of it with carb cleaner until it runs out clear seems to work really well. Don't get the little motor wet though. Let us know.

The charging circuit wouldn't effect idle speed any, unless there was a very large load on the alternator that would drop idle down 100-200rpm, but it wouldn't cause a high idle. I think you are right. It's a seperate problem.

As far as the high idle, check all the vacuum lines and the throttle position sensor. A vacuum leak most likely won't contribute to high emissions by itself, but it would cause a high idle. The throttle position sensor idle voltage should be almost exactly 0.96 volts. Other things you could check are:
intake air temp sensor. This sensor calculates how dense the incoming air based on it's temperature.
Whether the throttle is closing all the way. Maybe a binding throttle cable. Do NOT adjust the little screw that rests against throttle. That is factory set. The computer is responsible for idle speed based on the input of various sensors. Let us know.