For what its worth, I found Lexus customer service (nationwide, 800 number etc.) to be very helpful. Mine was certified used and I had a problem with my trans that the local dealer would never get to the bottom of. I complained to the national number a few times and they got the local shop to work harder on it and eventually they replaced my trans and everything is good and has been fine for a while.
My impression about them was that if you're reasonable and you can demonstrate that you've maintained your car well, they want to take care of you. If your car really has 42000 miles on it (nothing fishy about the mileage), it is unreasonable to think that a $40K Lexus that's less than 5 years old should have a serious trans problem. Lexus wants and has a reputation for great reliability and customer service and they want to keep it that way -- if you explain it to them like that I bet they will take care of you. I'm not saying they would pay for a fluid change, but if you did all of the above and paid for a fluid change and there was still a problem, I bet they would take care of it or at least offer you some help.
Mine is outside of the 3 years for my certified warranty but is still under the 100,000 miles. They offered me a significant break on another problem I was having. The trans thing started when I was still under the 3 years, but they didn't end up fixing until after the 3 years.