I would look at a couple of things to start with.
1) Is your snorkel air valve on the air filter box open?
It should be open to the corregated hose that runs to the exhaust manifold at cold start, then open to fresh air after warm-up. There is a thermostat inside the air cleaner housing that switches the vacuum source to change the valve.
2) Check the EGR valve on the top of the intake manifold to ensure it's operating smoothly and closing fully at idle. If its not, then it will cause stalling and idle problems.
3) The Coolant Temperature Sensor on the front of the intake manifold under the Air Pump senses your engine operating temperature. If the sensor is bad, or the wire are broken, basically the ECM doesn't know if the engine is hot or cold, and will not know what mixture to set the fuel injectors for. It can cause a cold engine to run really rich, and a warm engine to run really lean, idle high.
Sometimes they can have a "threshold point" where the engine runs really awful until it hits a certain temperature, then suddenly it smooths out like nothing is wrong. This sounds like your best bet.
You can probe the connector with a voltmeter and monitor the voltage across the two terminals. Taking off the Air Pump is the best way to get a clear access to that sensor. If the voltage is the same when cold as it is hot, then the sensor is probably bad.
4) Check your vacuum lines at the intale manifold for cracks, holes, pinches, etc. They all provide vacuum to individual sensors or valves that are controlled or monitored by the ECM that control certain functions of the fuel system. EGR valve, MAP sensor, AIR pump, etc.
5) Check the TPS (Throttle Position Sensor) voltage with the key on, but the engine not running. It should be 0.525V + - a few millivolts with the throttle closed. See pictures: (Note* second picture is with the connector unplugged. You will need to make some extender wires to get the voltmeter leads on the connector pins to check it while operating.)
