I just wanted to close this thread by explaining how the problem was fixed, that way if other people have similar symptoms they have a good idea of what the problem is in a lot less time than it took me.

I tested the MCS and knew it was good. All along I thought I heard it cycling, but what it turned out to be was the EGR solenoid. Big difference. I decided to take a chance and pull a computer from the junkyard in hopes that, that computer was good and my current computer was junk. Well, I put in the new $15 computer from the junkyard and everything works perfectly. The MCS cycles like it should and it runs like a dream set at the factory carburetor settings without tuning at all. So in short, my ECM was messed up and wasn't sending a signal to the MCS making it run like total crap. Thanks for all the help everybody!