MOTER STALLS WHEN AT RUNNING TEMP AND IDEL

id start with the ignition system

If you did not disconnect the battery and drain the voltage from the ECM, it could be using old settings when the problem existed.
When a problem occurs, the computer tries to correct it or find new settings to work around the problem. When you fix a problem you have to clear the codes and sometimes erase the memory from the computer to allow it to start back at the factory settings.
When you disconnect something and the check engine light comes on, the computer goes into limp mode and uses values for the sensors preset by the factory. The car will almost always run rich to ensure the driver can get back to a place for repairs.

try changing plugs and wires, if need be remove and clean idle air control valve, cause this is what controls the ideling.

My Pontiac Grand Prix is also a 99, it has 216,+ thousand miles on it, it runs great, idles good, I need to replace the oxygen sensor tho as it shuts off on me while driving or sometimes coming to a stop. You might try checking the fuel filter and pump as well.

do an internet search for "idle learn procedure" for your car and follow the steps. worked great for my 93 grand prix

I RAN INTO THIS BEFORE TRY THE IGN MODULE UNDER THE COILS WHEN THEY HEAT UP CARS QUIET AND DO NOT START

CHANGE FUEL FILTER CHECK YOUR UPPER AND LOWER INTAKE GASKETS OR THROTTLE POSITION SENSOR

seems to me there may be a problem with the transmission, because you say it runs fine in neutral and dies when you put it in gear!!!
only logical thing if everything else you mentioned has been ruled out!!!

Make sure your cooling fans are coming on when the temp heats up. Are you talking about a leak inside the car or outside? Inside is usaully a drain tube for the A/C stopped up. Outside, look for a water pump or intake gasket.

A cause for that would be an oxygen sensor getting wet, the one on the inlet side of the catalytic converter.