A chip and dyno tune may help, but before spending time and money on the dyno, you may want to address the surging idle beforehand. The tune probably won't cure the surging idle, as it is most likely caused by something else.
Check thoroughly for vaccum leaks, loose clamp/s in the intake tubing, anything that might possibly be the culprit. Carb cleaner sprayed in the vincinity of the suspected leak while idling may cause a stumble, meaning you have found the vaccum leak. Also, now that the motor is breathing more and you have made some significant changes, try adjusting the idle adjustment screw on the throttle body. Also, it could possibly be the IAC motor is not allowing enough air in or is allowing too much air to bypass the throttle plate. I found an IAC restrictor plate from a guy on stangnet that solved that problem on a friends car. The guy was selling them for next to nothing. Search for "IAC restrictor plate". Next, try addressing the C&L MAF. I have heard nothing but bad impressions from the people who have had them.
My car has a FAST system, and I can adjust the IAC P and D gain values to fine tune the idle. I'm not sure if the factory EEC will allow a tuner to do the same, but it's worth asking. :dunno: