First what engine are you talking about? If it is chain driven, then it must be the 2AZ-FE engine. If so, I do not understand why the chain would need to be replaced simply because the vehicle was unused for a few years. Also, the water pump on that engine is external and is not driven by the timing chain, so I fail to understand what changing the timing chain would have to do with engine temperature unless you did not put the serpentine belt on correctly and the pump is running backwards or something.

I also do not know why you say there is a problem with the temperature when you say the temperature is in the middle-----theat is where it is SUPPOSED to be. If you think your gauge is reading incorrectly, then that is what must be diagnosed. First, you must verify that it is incorrect by measuring actuall engine temperature with an infrared thermometer next to the temperature sensor. Then you must compare the actual temperature reading with the ECT data in the engine control computer to see if the computer is reading it correctly. If it is reading it correctly and your gauge is reading too high, then there is a problem with the gauge in the instrument cluster. If the computer is not reading the temperature correctly, then you either need to replace your temp sensor or repair the circuit between the temp sensor and the computer.

The hard starting could be caused by a whole bunch of things. You could be off on your cam timing. You may have installed the Crankshaft Position Sensor Plate upside-down. It could be something like you have a tank full of rotten gas if the vehicle has been sitting for 3 years.

If you are going to a mechanic that is advising really dumb "fixes" like leaving sensors unplugged to get your cooling fans to turn on, I would highly recommend going to a different mechanic.