I am happy to say that the ECU/TRAC upgrade was done today and I tested the car to see if I still get that hesitation and it seems to be gone!
I also spoke with the parts guy (his name is Lou) and he says that they don't order any spare TRAC ECU's since they cost them $1000 and Lexus will not pay for them until someone comes in for service, so you need to make an appointment first and then he'll order it.
Thus, if you want to have your ECU updated in Rallye Lexus, call them and speak with Sheila, schedule an appointment or tell her you want the ECU updated. Then speak with Lou and make sure he orders the TRAC ECU.
On the downside, today I probably had one of the worst service days someone can have.
1) She tells me that the service is going to take 1-1.5 hours so I should wait in the lounge, then 15 mins later she tells me that I'll have to leave the car there for a day and pick up a loaner.
2) She gives me a Ford Contour, since she says they didn't reserve a Lexus loaner for me (since they thought it's not going to take long). This Contour is one of the worst cars I've ever seen and driven...it looks like it just came from a junkyard, one of the wiper rubber parts is broken, etc.... I drive the car 200ft and then notice it has the "Check Engine" light on. I call Lexus service, she tells me to bring it back in. This time I get a 900mile old Ford Focus 4dr. This one is definitely a step up from Contour, but it's no Lexus (when the A/C is off and you're standing at the stop light, the whole car jerks every few seconds-I guess the engine RPMs are dropping too low)
3) She finally calls me around 2pm and says that the car is ready for pick-up. I come in hoping to get the keys and drive off. Well, it takes another half-hour before they bring the car around.
4) While waiting I went out to take a look at the car and noticed that they didn't wash it, so when they bring the car, I tell them it wasn't washed. It takes another half an hour before the car is ready.