Hi,
I have experienced the similar problem with my 2002 Rav. I did a bit of research on the net and found that the actual cause of this transmition problem is to do with the ECU/TCM and not the tranny itself. Have a word with Toyota and insist on a new ECU esp if you new tranny is still lumpy, they are aware of the problem! Also take a look at this forum,
http://rav4world.com/forums/viewforum.php?f=6 you'll see numerous threads of this nature.
Good Luck!