Basemnt flooded water heater wont stay lit ever since, taken out burner assembly severl times now stays on long enough to heat water then shuts down soon after.replaced thermocoupler and have to lite manually and when you close door goes out imeditally...

Clean the pilot sounds like its short /blocked . Also it could be the thermocouple needs replacing

I would try cleaning the thermo couple surfaces with some steel wool... Both where the flame contacts the sensor, and the electrical contacts. Even a small increase in voltage may be enough to hold the pilot valve open. Both black, and white soot on the sensor end, can act as an temperature insulator, lowering the output voltage.
As for finding the part numbers for replacement: http://www.reliancewaterheaters.com/media/48391/242117_RPPCR01111-Reliance-Parts-Catalog.pdf

The pilot lights then heats/sends a signal to open gas for burner then(burner)should stay on but if valve shuts the gas off,then have your unit checked. What ever you do,DON'T MESS WITH IT IF GAS/FLAME ON!!!!!. These systems come with a safety feature that allows gas to go on only when safe!!!!

Maybe the gas control valve thermostat is bad.
http://waterheatertimer.org/pdf/How-to-replace-water-heater-gas-valve.pdf

Thermocouple is good because pilot stays lit.
The burner goes on so gas pressure is probably good.
http://waterheatertimer.org/How-to-troubleshoot-gas-water-heater.html#intellivent

Replace gas water heater
http://waterheatertimer.org/How-to-install-gas-water-heater.html

If you need further help, I’m available over the phone at https://www.6ya.com/expert/gene_9f0ef4df2f9897e7

Get more fresh air to the unit.
Clean the air intake/ flame trap/ flame arrestor located on bottom of tank.
http://waterheatertimer.org/images/Flame-trap-inspection-325.jpg

Post question on pro water heater forum.
http://www.thetankatwaterheaterrescue.com/forums/forum3/

Add a comment with type of gas control valve, for possible troubleshoot.
Copy following link to read service manual by type of gas control valve:
http://waterheatertimer.org/How-to-troubleshoot-gas-water-heater.html#intellivent

If you need further help, I’m available over the phone at https://www.6ya.com/expert/gene_9f0ef4df2f9897e7

There may be a draft blowing out the pilot. Place some fiberglass insulation inside the cover for the burner or pull down the insulation from inside the jacket just over the burner opening.

Manufacturers say to replace water heater after a flood.
Flooded water heater can be repaired by replacing parts but warranty is voided.
And if water heater reached gas control valve, then gas control has to be replaced >> possibly the gas valve eco tripped.

I don't know how effective cleaning burner parts will be, since a small spider wed inside some of those tubes can cause water heater not to function. Small obstructions cause big problems.
I'm sure the plumber cleaned it out real well.
Find manufacturer using label on side of tank, find manual with parts diagram, and order burner parts.
http://waterheatertimer.org/Water-heater-manufacturers.html

It might be cheaper to install a new water heater yourself from box store
http://waterheatertimer.org/How-to-install-gas-water-heater.html

I read one article:
http://www.diychatroom.com/f7/rheem-hot-water-heater-pilot-burner-not-staying-lit-65755/
Guy has water heater that filled with water.
He says: "I decided to feel around. As soon as I put my finger into the hole under the burners I hit water. The air intake passage was filled with rain water, effectively chocking off the fresh air. A few minutes with a siphon tube cured the problem and the water heater works normally again."

Absolutely feel obligated to upvote the help.
Or take advantage of fixya expert assistance live.
For a price, expert works with you while you work on water heater or any do-it-yourself project.
Fixya is always less expensive than a service call.

Hi,
Thermocouple is getting weak... the extra heat from the main burner will keep it lit but after it goes out the thermocouple will then shut down..
Replace the thermocouple...

heatman101

When you light the pilot lite you have to hold the button down until it gets the element hot enough to stay lit. If you hold down the button and lite the pilot and let it go right away it will go out. What to do is hold down the button and lite the pilot and continue to hold the buttn down for about 45 seconds to a minute then let it up very slowly and you will see if it is going to go out by the flame getting smaller as you let up on the button. If it does start to get smaller conitnue to hold it again for a few seconds and repeat the process of letting it up slowly. when the control element gets to the right temperature it will stay lit then turn your valve to "ON" and the fire will start up and continue to heat the water.

It sounds like your main valve. The diaphram may be loose fitting or it has a small leak.