Checking the IACV is a good thing to do in general. I had my setup running for years and it would occassionally surge at stop lights (embarassing

). After CarlH mentioned it in a post, I went out and toyed with it and realized that the set screw was way off. I set it per the FSM and the surging stopped. It started surging about a year later and I rechecked the screw and it was fine. Then I traced the 1-inch air line and saw that it had rubbed against a hole I cut in the battery tray area causing a cut in the line. I replaced the line and the surging stopped.
As for checking the timing, look at page EN-15 of the FSM. It describes how to set the base timing. The ECU is going on the assumption that the CAS is set such that the base timing is 15 degrees. (3rd white tick mark from the orange one on the crank pulley) If the timing is off by say 5*, the entire timing map in the ECU is trully off by that same amount. Having too much or little timing on decel can be just enough to cause popping and sputtering. So get a timing light out and verify the base ignition timing.
The FSM says to disconnect the throttle position sensor (TPS) plug from the throttle body to set the timing. Whenever I do this, the idle speed bounces all over the place. So I have to leave the TPS plugged in. Mine is a S1 so an S2 might be a little different. Try it both ways and see if it makes a difference.