As far as the alternator goes, I'm running a one-wire GM unit on mine and it works fine (I know, it's a Chevy part, but one-wire alternators for Fords are twice as much).
Again, you said you were getting an air bypass code...what is the code number? Are you still getting the code?
You should be idling at around 600 RPM.
Have you checked the basics.....ignition timing, check the engine vacuum at idle, clean air filter, check for vacuum leaks. Many times it's the basics that will get you.
Other tests you can do quicly and easily just to rule items out include testing the ISC and the TPS. Check the Idle Speed Control solinoid by disconnecting it while the motor is running. The RPM should drop way down or even die. Check the TPS to make certain the voltage changes smoothly throughout the throttle range. They often develop 'flat spots'.
As far as your engine running with the key off, that's a mystery to me. Perhaps a bad ignition switch?
You had said you head a click near the computer. Check to see if it's coming from one of the relays. You computer is solid state, and has no moving parts. Most likely it's a solinoid mounted near the computer, and that might also be a key to your problems.
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