I am not a transmission expert, but in doing some quick research for you, I have come across a few people who mention that a transmission reset fixed their jerky shift issues.
Now while that might not be 100% the same as your case, I think that maybe your transmission doesn't know you put in new fluid and filter. Maybe a reset will work. Posts I have seen say that a battery disconnect for 30min resets the trans ecu. I'm guessing that can't hurt anything.
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