I can't believe (ok, maybe I can) that Autozone charges close to dealer prices on the IAC for the 4G6 engines (I paid $330). When I had my '93 GS, I went with the dealer IAC, since there was a revision to the design to make it more reliable.
Anyway, test the IAC you put in for peace of mind. I've had too many turbo DSM guys tell me horror stories regarding aftermarket IACs. I believe it could be that alot of aftermarket companies base their IACs off of Mitsubishi's original design, not the revised one. Plus, if there's an issue that arose once you changed the IAC that wasn't there before, chances are the IAC you installed could be defective.
Another possibility is that the plug or wire for the cam sensor could have been loosened during the IAC replacement. That would most definately cause issues, since the ECU would basically be left to 'guess' when to fire the injectors and spark plugs. Your timing could be fine (especially if it didn't run rough before), but the ECU might not know that if the signal to the cam sensor has been severed.
While I'm still thinking about it, what is the condition of the idle set screw? Those tend to get messed up, since they're made of soft white plastic. The threads and/or o-ring could be shot. And they're cheap to replace.
Hope this helps.