Some 1999 Jetta GLS models with 2.8-liter engines may run hot or overheat. In some cases, the hot running engine may be accompanied by an illuminated Check Engine light, with coolant sensor codes P0116, P0117 or P0125 logged in PCM memory. One likely cause for all the trouble is the plastic water pump impeller cracking or completely separating from the pump shaft.
To make the diagnosis, use an infrared thermometer and compare the temperature of the radiator to that of the cylinder head. If the radiator temp is significantly cooler than the head, that's your cue that there's very little or no coolant flow through the engine. Removing the thermostat and thermostat housing should give you a clear look at the pump impeller. If it's damaged or spinning on the shaft, replace the water pump.