just read this thread, and from a fresh point of view, sounds like a maf problem
lexus's solution may not solve the problem. the ecu is telling them its starting off in 2nd, but not why. if the problem was before the signal reached the gear box, the new gear box would start in 2nd anyway.
my gs300 flies from a standing start, hot or cold(ish)
stick the car in "L" and see how she pulls, should be very strong. if you cant select "L"(1st gear) then you know its the gear box
(do this once the car starts giving you trouble)