I seem to be having the same problem. I couldn't go over about 50 mph, then it went to about 35mph limit, with a LONG gradual ability to attain 45mph.
The filter was changed. A mechanic friend hooked up his laptop diagnostic tool (best shop in the area where I live), and said he wasn't getting any codes, and he thought maybe it was the throttle position sensor, and advised I take it to the nearest Toyota Dealer (nearest Lexus is over 2 hours away).
I changed the TPS, and the RPM limit went from 2500 to about 3100, and I can not get to 50mph or better within 2/10 of a mile.
The latest suggestion by a different mechanic who's looked at is the idle control, but I do have my doubts about that one....