Your issue may not be transmission related.
Suggest you get a scan tool that can read real time data on the car and verify the coolant temperate and fuel trims. Far too often people check the coolant temps on newer cars and see a figure close to 180F and determine the coolant temp is fine. This is not the case, most of the newer cars need to run at about 200-205F for proper performance. This is where your engine should be running as far as engine coolant temp. Do not be fooled by the fact your engine may have a 185F thermostat. Your coolant temperature sensor is located at the output of the cylinder head coolant, not near the thermostat so this is why there is a big difference between the thermostat temp and what the coolant temp sensor reads.
The other thing I would suggest you do is some research on the 2.0l catalytic converter issues. You may need to get under your car and take the palm of your hand to and hit the catalytic converter to see if you get a rattle of internals from the converter.
Not sure if the early cars were as prone to the converter problems, but it is worth checking out.
You may also need to buy an exhaust back pressure tester to confirm you do not have an exhaust restriction.
Something like this is what you would need to test the exhaust back pressure - Tool Aid 33600 Exhaust Back Pressure Tester - Amazon.com
The other thing is do you know the history on the car very well? It would not be the first time a camshaft would be off by 1 tooth causing a loss of power. This should be a pretty easy check by just removing the cam belt cover and confirming the camshaft position is correct.