My X stopped in a hood-level pool of water and flooded to the seats.
The vehicle just would not start after that and d gear also could not move from Park to Neutral.
The guys at the workshop have not provided a solution yet and are suggesting we change the brain-box..
Any ideas here people?

Hopefully you didn't suck in water to the engine and hydrolock it. You could have potentially ruined the block in that case.

Hard to say but the ECU is a prime suspect in the case for sure as it sits lower in the vehicle and has happened to others once it get's submerged in water.

how did it just stop in that deep of a pool?

if it was hood-level, it was above the air intake (inside the driver's fender), so you probably sucked up some water and locked the engine

in which case, it wouldnt matter whats wrong with the trans, because your engine is royally screwed ....

...so, how did your X come to be in such deep water?

It was one of those really rainy days in a coastal ares with deep pot-holes in the roads.
How much does a new ECU cost these days if indeed I have to replace?

There is a used one online here for $150:

http://www.justparts.com/AutoParts/2005_NISSAN_XTERRA_ENGINE_COMPUTER_ECU_ECM_45753_M ILES/19814200.html


Otherwise a quick search should give you a good idea.