Old williams furnace / basement flooded. Replaced gas valve,pilot and thermocoupler all new. Now fires up heats house everything looks good then goes off and pilot goes out.

As in any flooded condition it is always best to call for on site professional service and have the complete furnace checked out. It is the only way to be sure of your safety. Also have them check the heat exchanger for cracks especially if it is the old drum type heat exchanger.

Your advise is best but I called the expert and it will cost 1500 for a new furnace (does not include installation) there is also some asbestos wrapped around some of the duct work that they understandably refuse to work around until I have it professionally removed who knows how much that will cost.
It is a very old house and getting colder as we speak.

I understand your position on this hvac1000 and I thank you for your good advise but I joined ask me help desk because I need some technical advise to resolve this issue myself.
I would appreciate any help,advise or similar past experiences that I can get.

Watching the pilot light closely when the gas valve shuts off its almost like it sucks the flame away from it, the pilot goes out with the main flame.

You replaced the gas control, but did you set the pilot & main gas inputs correctly? If the pilot is over-fed, the flame tends to lift a bit, making it vulnerable to snuffing. If set too low, the secondary combustion air may divert the flame from impinging on the thermocouple. You replaced the pilot - is the proper gas orifice in place? The main gas input should also be checked/adjusted with a manometer. Pic of common combination gas control shows adjustments for pilot gas input (under silver screw) and main gas input (under brass screw).