have found the best way to check for air leaks (vacuum leaks) is to squirt brakecleaner around any possible leakage areas. If there is a leak the idle will rise slightly. Start with the obvious things like pipework and rubber boots etc, try the split line on the bottom of the plenum chamber, Skylines are known to leak here, also check the intercooler for leaks and all pipework joints.
To adjust the idle speed with the idle speed screw on the back of the plenum chamber you have to disconnect the Fast Idle Control Valve and the Idle Speed Control Valve and also the tps (good practice to check this fisrtly for <0.55 volts at fully closed. You can then set the base idle to around 750 rpm. Re connect everything and the ECU should hold the idle at 800 rpm.
However the most likely cause of your problem is a blow off valve venting to atmosphere. This is because the ECU acceses the amount of air inducted and sets the injector duty cycle accordingly to maintain the correct air/fuel ratio. Once the BOV dumps this air the mixture becomes overly rich until the BOV closes and rpm etc equalise. My R33GTS25t did the same thing. Once I plumbed the BOV vent back to the turbo inlet (AKA stock) it was fine again.
Finally the reason the Super FC doesn't use a map sensor is because Skylines don't have one, they just rely on the Mass Airflow Meter. This is also a common cause of many "Skyline Probs"