Volkswagen Repair: Stalling problem, coolant temperature sensor, engine coolant temperature sensor

Question
Hi Rocky
I recently had the engine in my 2000 VW Jetta GLX(VR6) replaced after flooding the last one thru a modified intake. Soon after that it started stalling after I had driven for a while. The CEL eventually came on and when I scanned it indicated Intake Air Temperature was too high. Now its stalling more often and then I can't start it till its cooled off for a while. Cool off time was 5 to 15 minutes initially. Now its lasting hours. My mechanic took off the plastic covers to check if there were any loose wires, broken hoses etc and couldn't find anything. There was spark in the plugs and didn't think it had to do with the fuel pump. He seems as baffled as I am and rather reluctant to work on it. Please help.

Answer
Hi there Kei Kei;
The throttle body is cooled with engine coolant.  The engine coolant temperature sensor is a big problem sometimes too.  Has the cooling system been properly flushed, and then refilled with a vacuum?  This causes more overheating, and drivability issues that just about any other single thing.  (1) replace the "ECT."  (2) Flush, and refill the cooling system with fresh coolant, and make ABSOLUTELY certain that the proper method is utilized...evacuate, and then re-fill.  (3)  inspect the coolant flange, at the end of the cylinde rhead for leaks, and finally inspect the big coolant pipe from the back of the water pump to the coolant flange carefully for leaks too.  Many VR6, especially "AFP" style VR6 engine drivability issues derive from improper cooling system issues.  Good luck, Kei Kei.  I hope this helps get you back on the road!