I'm glad the filter change worked/helped. I would still take it to the shop that rebuilt it and tell them what was going on, what you did, and ask them if they could do a few checks.
A tidbit of info...Changing the fluid in an auto trans takes FAR more than dropping the pan and replacing a few quarts. More like an expensive Auto Trans Flushing Machine and typically 5 gallons of fluid for a flush and fill a full size vehicle trans. About $120 around here in NW Iowa...of course I have a Buddy with an auto repair business, so it costs me less than that if I need it on any of my vehicles.