I hope this helps with the list.
For those who are not certain if they should replace their AT fluid filter. Here's a view of a filter that had over 120k miles.
As you can see the filter is a fine metal mesh which can be cleaned. This also means that this filter although is fine, it has less microns of filtering than a paper one which also means that the filter is mean for bigger particles so metal power will pass through it. Most of y'alls filters will look like this. Simple brake cleaner will get this clean.

 

Pulled from the FSM:
Like I had stated before the TCM stores shift patterns based off on driving patterns. Meaning Pedal position and fluid temperature are two main inputs that the TCM will see.
Any issues with Throttle cleaning will change these patterns, any bolt ons will change pedal patterns changing shift patterns.
Another observation is fluid temperature, under lower temperatures the TCM will increase fluid line pressure thanks to Motorvate I'm able to monitor my ATF temps and they stay between 150-190s with the cooler depending on my driving. With the cooler I see cooler temps since it's no longer connected to the radiator it never gets to see the same temps as engine coolant 180-213 degs which could mean those with coolers benefit from added pressure since the fluid would never get that hot. I understand atf proper temp is necessary however keeping it under 200degs I suspect would be key for proper shifts
PS for those who have gotten a high temp code these are triggered at 293F

Would be interesting to see any members who have Trans coolers chime in if they go through some of these issues.