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the other independant recommended I either only change what's in the pan or don't change it period, stating that I may do more damage harm than good by flushing out any particles that may sort of be holding things together


Wow, that statement is frightening. We put about 15K miles per year on our vehicles. Every 24 months I buy enough Amsoil ATF to flush the entire system and change the filter (although in the Runner I dont believe you have a filter, just some sort of screen). I have never had a transmission related problem.