I just spent almost 4K USD fixing my 01 VW jetta 1.8t and the check engine light still comes on and now it takes excessive time for engine to register temp on temp gauge and heat is unusually lower temp now/doesn't heat up all the way after driving 20 miles.
If you are having a heat issue and the engine won't heat up, make sure they used at least a 195 degree thermostat. Next, with the engine warm, running, and the heat on, feel both heater core hoses. Both should be hot. If one is hot and the other isn't, flush the heater core. If both are hot, check the blend door.