4EAT rough downshifting

The car: 2009 2.5 subaru outback with 4eat and vdc. with little over 100k miles.

When the car is warm and gearbox too the downshifting during braking at a traffic light for example goes quite rough from 3rd to 2nd and 2nd to 1st. When accelerating the shift from 1st to second is smooth, from 2nd to 3rd is rough again. 

When arriving at a roundabout (through speed for 2nd or 3rd gear) it seems the gearbox is in doubt and at last moment dups it rough in 2nd. Shifting with the steering shifters is rough as well.

When cold it drives fine. 

Now it is due to atf change in 3k miles. Now the questions:

1. Just replace the ATF

2.  Flush the ATF

3. Flush ATF and remove bottom and replace filter

4. Flush ATF, replace filter and whatever else !?!

It gave ones an error on atf temp sensor input low, never ever gave it again (10k miles ago), it was coincidently with an exhaust leak at center to front pipe connection.