Posting this here, too. Just in case somebody is doing a search on different search terms.
UPDATE:
Transmission flush performed with 12 quarts (?) of World Standard automatic transmission fluid.
RESULTS:
The shudder is 98% gone. From the third to fourth (?) shift its 100% gone.
It slightly shudders between 2nd and 3rd on slight uphills and if I'm not really pressing on the throttle and just leisurely driving up slight uphills. Weird. If I didn't have this issue prior, wouldn't notice it at all.
Shifts much better, as somebody mentioned before after they had this done - like butter.
I also had a slight whine upon decel (from 35 to 0, whether in neutral or in gear) and that has pretty much disappeared, too.
The flush was $350 with a $30 dollar discount, so $320 out the door. They did the whole monitor temperatures and computer when going through the flush process. For a simple flush, was rather complicated. Reason why I didn't want to mess with it myself.
CONCLUSION: Complete transmission flush worked for me. 2006 4Runner Sport w/ 150,000 miles.