I wonder if there is a short in the cooling fan? Perhaps you could pull the cooling fan relay and take it for a spin to see if you hear that thump again. Make sure the engine doesn't overheat and run the heater to draw some heat out from the engine if necessary. Also check the fan blades to insure there is no blockage.Another thing when its beginning to stall I still hear that loud thump under the hood. It sounds similar to when my ac engages in the Jetta. But I don't have the ac on, its not charged
If you quickly want to check the fan to see how it sounds when it comes on, just pull the plug to the engine coolant sensor on the thermostat housing. It will set a code, but you can clear that later by disconnecting and reconnecting the battery.