I have a 1998 Pontiac Bonneville with 53,000 miles. Last year the transmission clunked (noisy and vibration) on shifts, I changed the transmission fluid and filter and it went away. Now it started “clunking” on shifts, but goes away after several miles of driving. Maybe related to heat or?? Is a transmission overhaul necessary?
Is the fluid level correct?
Could still be foreign matter (dirt or metal shavings?) moving around.
Did you see any metal in the filter or fluid when you changed them?
Perhaps dirt is getting stuck in a shift solenoid or the pressure control solenoid may be worn.
Sometimes an extra fluid/filter change can correct this.
Probably worn 2nd gear clutch packs, Does it clunk every shift into every gear or just the first shift. At what speed, does it clunk if accelerating quickly, does it hesitate or delay shift. Does it clunk on downshifting, does it creep at idle or not. Are you using the correct amount and type of fluid? They all have different modifiers for friction. I would also change the fluid and make sure the tranny cooler at bottom of radiator is not getting blocked because you haven’t changed coolant. Heat is generallly what destroys the tranny.
I would scan for codes first.