Transmisson

I had the same problem when the engine was hot. I deduced that the tranny was hard shifting because of a vacuum leak. I plugged the vacuum at the EGR to test and the problem went away. Vacuum leakage- through the EGR balloon was causing the transmission to not receive enough vacuum for a smooth shift. So it is worth your while to look at the vacuums.. Hope that helps.

The "clunk" sound is likely coming from the two bushings that support the rear differential. The differential is torquing when the tranny shifts, The worn rubber bushings are causing metal to metal contact which makes a loud "clunk". These are reasonably cheap and not too difficult to replace. You will just need to lower the differential to remove the old bushings and drive the new ones in. Hope this helps!