Thanks for your message. Converting back to the manual is definitely possible, but it requires several modifications. You need to buy a manual gearbox, install new gear wiring, change the brake pedals, remove the clutch pedal, and replace the centre console. Additionally, the gear foundation and both drive shafts would need to be adjusted, as auto and manual transmissions have different lengths (at least in the Prado 92/94 models). There is also a chance that you may or may not need to replace the ECU card.
I made a northern area trip in July last year when my Prado was still manual. The manual was a treat on mountains, even better than my Fortuner Sigma with pedal shifters. The manual transmission gave me much better control, especially on descents. I also have doubts that an automatic transmission Prado would perform as well, even with the option to use 4WD to slow down on descents.
An automatic gearbox costs around three lacs, whereas I checked that a manual gearbox costs around 1.5 lacs. However, while an automatic transmission costs nearly twice as much, converting back to manual involves additional work such as ECU adjustments, rewiring, drive shaft modifications, and console changes, which could even out the costs.
If you're serious about off-roading and control matters more to you than convenience, switching back to manual might be the better option. However, keep in mind that driving a manual as a daily runner is not comfortable at all. If your primary concern is resolving transmission issues, you could consider fixing or replacing the automatic gearbox. But if the priority is the northern area trips, then go for a manual swap.
Let me know if you’d like to discuss this further over a call. I will PM you contact details, and I'd be happy to share my experience!