My engine had similiar irragular behaviour 2 monthes ago. While driving on the freeway using cruise control, the car suddenly slowed down for no apparent reason and would not speed up even if I floor the pedel. After about 3 trys the car would suddenly down shift and speed up.
Similarily, at stop and go traffic the engine would rev up by it self for 1-2 seconds, then going back down to 300-400 rpm, then surge again, and then back to normal. During all this time I had to firmly apply my brake so I won't rear end other vehicles.
Had my problem checked at Precision Toyota of Tucson (they are very professional nice people), the problem turned out to be the left crank shaft positioning sensor. During my last timing belt change (not at Precison Toyota), the mechanic did not properly seat the sensor wire into it's groove, causing the wire to rub against the timing belt and caused a huge cavity, totally destroying the sensor. Precison Toyota replaced the sensor for $375, parts and labour, and the problem went away. After some arguing, I got a full reimbursement from the timing belt shop afterwards.
This is just my case and might be different from yours. I thought I'd like to share it with you so you can be prepared when dealing witht the Lexus dealer.