Transmission quit shifting after going through a shallow puddle

. Fluid is full, no puddle.
Most likely the problem is with the transmission itself. It could be an issue with the transmission linkage, the shift forks, or the clutches inside the transmission. You will need to have a transmission specialist diagnose the problem and determine what repairs need to be done.

not knowing the quality of workmanship used in the engine rebuild, it is difficult to answer exactly what is wrong
plugs and leads will not be faulty
I think the clue is in the remark about the carby being replaced and it ran a bit better
that indicates ,along with the very rich settings, that it could be an valve timing problem
I suspect that the cam shaft lobes are damaged or the timing chain gear is loose on the cam shaft
running well in the beginning and then slowly failing all points to the cam shaft lobes, cam followers or loose cam gear

Jorge, as richie46 recommended check trans, fluid level. At higher mileages,150,000 the automatic transmission may not shift correctly. This can be caused by the throttle position sensor out of adjustment or a shift solenoid needing to be replaced. Typically the transmission does not need to be completely overhauled.
"I hope this helped you out, if so let me know by pressing the helpful button. Check out some of my other posts if you need more tips and info."

You have water in or on the trans. control module. If water got inside the trans. you will see a gray color looking fluid on your trans. dip stick.

I don't think overheating of the engine has much to do with the transmission, either automatic or manual. If you have an automatic transmission, did you check the fluid? Sometimes low fluid stops certain gears from changing, as the torque converter doesn't have enough fluid to pressurize the servos to engage the clutches.

Check for a possible cold start injector problem or a possible motor or transmission mount that is loose or broken.

Could be a long list of things.
Its too late for a filter change. Doing that now would probably make matters worse.
The trans uses electric solenoids and a pump to apply pressure to the clutches. So either could be faulty given the age and mileage.
I'm not sure if the shifting problem is connected to the shift indicator lights problem.
You may need to take it to a trans shop to find out for sure. And they will not want to touch it with that many miles on it.
A regular mechanic might be able to do a pressure test on it to at least find out if it is the pump or not.

Hello. Welcome to FixYa. I am Toyota Ed, and I will be assisting you today.

The Overdrive function allows the transmission to shift an extra time, sort of like selecting 5th gear in a 5 speed manual transmission. The Overdrive, when used, will save you gas, as the engine is no longer maintaining a high RPM at normal driving speed. Look at the tach whilst driving about 45 mph, and engage/disengage the OD. You will see the tach RPM raise when the OD is off.
More RPM = lower fuel mileage,

The ECT is a different circumstance. The ECT button is used primarily when you have a heavy load in the car, or are towing something. All the ECT button does, when it is engaged, is lengthen the shift points as the transmission upshifts. Normally, the transaxle will shift into 2nd gear at 18-21 mph. When the ECT is engaged, the transaxle will shift in the area of 22 -24 mph. In short, the ECT just makes the time to the 1-2 and the 2-3 upshift longer, to compensate for the additional load being carried/towed.

I hope my assistance answers your question.

Thanks for choosing FixYa today!

Acutally there is 3 position settings for the transmission selector, the power setting which changes the shift points higher ,more rpm's, center position basic auto selection the transmission selects the best driving gears based on your habits, and the comfort mode which shifts the transmission easily and smoothly, no high rev shifts, best for good fuel mileage, but if you need to get on it it will go.

It sound like your transmission linkage needs to be adjusted.
Its hard to tell what is wrong with the tachometer, without knowing if it is original, an aftermarket, or if anyone has messed with the wiring.
I would suggest buying a repair manual (Haynes is about the best).