You can send the car to Puspakom for inspection. They will give you a report on the car condition. When you transfer the car to your name, you need to submit the Puspakom report to JPJ.

Once I watch on tv, they showed how Puspakom inspect a vehicle and found it was a kereta potong.
They showed where the joining parts are and explained how they do the joinings.
Maybe that was just for show on tv.

You must be experienced enough to check if the car has been flooded before.
1. check under carpet for mud stain
2. check inside the headlamp to see if got mud stain
3. check car seat for mud stain

FYI, those cars that were flooded before, will be sent to professional cleaner to clean the car so that people cannot spot them. But due to human error, they may missed some area that they cannot clean.
You need to get someone who know where to look or check for those areas.