I was finally able to get rid of the P0125 code!
Basically I just performed a Zero-Point Calibration, then did an A/F sensor setting drive and disconnected the battery for a few minutes, and it went away.. With that said, I am just going through actions erased my code, I am not saying that it is an official procedure or anything, so take it as you will... Since it will cost you close to nothing, I would give it a shot.

P.S. You know how hard it is to drive for 7 minutes at 40-55 mph in Michigan? You either have a 70 mph speed limit, or a darn red traffic light at every intersection! I've spent an hour cruising around just to find the place to perform the drive pattern.. Whew...

Hope this helps and best of luck!

 

What is the zero point calibration? what year and model is ur Lexus? That's awesome, I'm in Oklahoma and have plenty of room to do the A/F sensor drive. until that's done codes will keep popping up even after you reset them? I've done the disconnect of the battery and pulled the ECU FUSE. but the check engine light came right back on!!

 

Mine is 2000 Lexus ES300.

Zero Point Calibration is basically as it states - it calibrates initial parameters of your ECU. It should be done after each major engine, drivetrain, suspension or brakes repair.
Does your car already have an OBD2 port? You can check it by the sticker under the hood. If so, follow steps below.

Here is how you do it:

1. This is vital for the whole procedure: make sure that the vehicle is on a fully leveled surface (up to 1 degree). Then, make sure that wheels and the steering wheel are completely straight, the vehicle is in Park (Neutral for manual), and that the e-brake is applied. Do not vibrate, shake or tilt the vehicle in any way during the procedure.
2. Disconnect the battery for a few minutes, and then re-connect it.
3. Get two small paper clips, straight them out and insert one of them in CG pin (pin 4*), and the second one in TS pin (pin 13*) of your OBD2 port. Bend them over each other to create a sort of a button. *Those worked out for me, but may not work for you, please send pictures of your OBDII and Diagnostic (under the hood) ports.
4. Turn the ignition switch to the ON position, without starting the car.
5. Within 8 seconds, connect and disconnect your paperclips 4 times or more. After that, your ABS light should start blinking.
6. Wait a couple of seconds to confirm a steady blinking light and then switch the ignition OFF.

Now you have successfully erased the old calibration data. Follow next steps to record a new one:

1. First step is the same, make sure that the vehicle is leveled. Ensure that the ignition is OFF
2. Connect both of the paper clips, and while holding them, turn the ignition to ON position, without starting the engine. While holding paperclips, you should see the ABS light flashing again, but in a different manner.
3. Wait a couple of seconds to confirm a steady blinking light and then switch the ignition OFF.
4. Disconnect and remove your paperclips.

Now you have successfully programmed a new calibration information to your ECU. To confirm it, go for a ride, drive the car for at least 15 minutes in a start-stop traffic. That is all there is to it.

Hope this helps and best of luck!

 

^^^
This procedure is non-existent on the OP's model.
A simple disconnect of the battery would clear/reset memory on these older models.

What you can do is eliminate the electrical part of the shifting to narrow where your issue is.
There is a connector called SOLENOID wire connector located just above the PRNDL switch connector on the transmission. (see pic)
When you have this disconnected, drive it and hydraulic pressure will take over shifting properties eliminating the electrical side (ECU, SOLENOIDS, etc...)

If you have all 4 gears shifting, then you're problem is on the electrical side.
If you are still stuck on 3rd gear, its a mechanical issue in the transmission.

 

No Zero-Point Calibration? That is good to know..

About solenoids connector - am I not getting something, or you will do no good by unplugging what seems like solenoids #1 and #2? You will just prevent the transmission from shifting at all. You can utilize a much less "painful" technique to test those out by using a scan tool, which I believe was already done, judging by previous posts.
Again, there are some codes that would prevent the car from going into the overdrive, and it really seems like it is indeed your issue. So you need to check all the codes that your car has. When is it returning from the "shop"?

I may very well be wrong here, so, Nad1370 - I would really appreciate your response, thank you!

 

Its an old school trick.
Disconnecting the solenoid connector to shift via hydraulic pressure.

You have to understand how transmissions work.
Its relatively all mechanical in there.
The valve body has check ***** and accumulator springs that realease thru high pressure when shifting
Shift solenoids are added to provide efficient smoorh shifting.

Dont worry, the transmission WILL still go thru the gears fine as long as there is no mechanical problem inside.
A harder than usual shift is expected but wont do any harm.

 

I would have never believed that such procedure would not cause any damage.. That's a great trick, thank you!

 

Stop clearing your engine codes. Get on the highway and drive the car for 10-15 minutes. Do that a couple of times and keep checking the codes. Buy any scanner that can read codes

Likely problem: your car is not shifting because you have a problem with your A/F sensor, also known as an oxygen sensor on the upstream OR a knock sensor. Both of these will put your car in « limp mode » where it doesn’t shift into overdrive.


One more thing: coolant temperature sensor code is almost always a code that pops up with other codes and is not actually accurate. Make sure you fix the other codes first.