Why is my Toyota Highlanders Engine Knocking/pinning and other.

I bought my Highlander/Kluger MCU26R with a 3MZ-FE V6 Engine 3 years ago. It had 18.500 km on the clock. Soon After I found out that the engine starts pinning when it reaches normal operating temperature even though the car has been filled up with 98 octane fuel. Then I noticed that there are problems in Shifting gears. For example the engine is chasing 1st gear when the speed is under 20kp/h, also erratic shifting. No trouble codes ever come up. The Engine light also never shows up. The MAF and OCV voltage supply and output voltages is OK. Only ETPS (throttle) maximum opening angle is 49% when the accelerator pedal is to the floor. The ETPS (throttle) has been replaced but the problem is still there. Engine pinning, erratically shifts gear, well under power. Lately more problems appear like these ones: When the car is parked for about 10-60 minutes the temperature is almost cold the car cranks and it almost starts but then is stalls. Only from the 2nd time does the car start properly. Please do you know what the problem is and how to fix it? Any help will be appreciated!