After burner turns off. smell of gas is noticable. checked, by turning off gas at control valve assembly. if gas is shut off, no smell of gas, but as soon as you turn on water heater after burner turns off, a heavy smell of gas exists.

Check for error codes and service manual on following link:
http://waterheatertimer.org/How-to-troubleshoot-gas-water-heater.html#intellivent

Replace gas control valve
http://waterheatertimer.org/How-to-replace-Honeywell-gas-control-valve.html

Gene:

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Shut off the water and gas to the heater. Drain the heater. Disassemble the gas line to the heater starting at the Union and working to the gas control. Disconnect thermocouple, burner and pilot tunes from the bottom of the old gas control. The old control will screw out of the front of the heater. Grab the entire housing of the control and twist counterclockwise to remove. Perform new gas control install and connections in reverse. Remember to apply at least 4 wraps of Teflon tape on all threads before assembly. (Teflon paste may be used) Do NOT put any sealant on the thermocouple,burner tube or pilot tube connections (these are compression connections, make them fairly snug.) upon completion, fill heater, turn gas back on relite and check for water or gas leaks

It depends on the model but AB on most of the AOS the A & B LED's lighting up usually means ignition/flame failure.

Ignition/flame failure:

The gas control valve/thermostat has reached the maximum number of retries (3) for ignition and is currently locked out for one hour. Cycle the power to the water heater off and on to reset.

Basic troubleshooting/solutions:

1 Ensure flame sensor is making good contact with the burner flame and ensure flame is steady. Also ensure supply and manifold gas pressures are within the requirements in the installation manual.

2 Gas supply is turned off - pressure is too low. For low gas pressure, consult with your gas utility.

3 Ensure the flame sensor is clean - use fine steel wool to clean the flame sensor.

4 Check igniter assembly plug and the socket on the bottom of the gas control valve/thermostat for good connection. Replace igniter assembly if the plug is worn or damaged. Replace the gas control valve/thermostat if socket is worn or damaged.

5 Replace igniter assembly.

If this does not apply to your model then here is a link to the instruction manuals for all models:

Residential Gas

You replaced the gas control valve thermostat, and the burner assembly.
You bled air out of gas line.
Assuming the gas control valve is functioning correctly, the last things would be gas pressure, air intake, and vent draft. If gas control valve is electronic, check outlet with circuit analyzer and make sure ground is connected.
Also if water heater is located in hot attic, or tight house, these things can cause water heater not to function.

Open following links for some resources and illustrations:
http://waterheatertimer.org/How-to-install-gas-water-heater.html#troubleshoot

Is this the newer style with closed combustion chamber. If so I would check to make sure that spark ignitor is working. If not it will need replaced. If ignitor is workingthen loosen compression nut on line to pilot and temporarily depress button on gas valve to make sure you have gas at that point.If you have gas there and tighten compression nut to pilot back up and it still won't light then you will need to remove screws that hold cover on burner compartment.Shut off valve to gas supply and remove gas line from gas valve remove pilot and thermocouple lines. Slide burner out ofcompartment and clean it .Remove nut from bottom of pilot assembly and clean out pilot orifice. Blow through pilot line to make sure it's all clear
Reassemble everthing using teflon tape or pipe joint compound as needed.Turn gas supply valve on and check for leaks.Set gas valve control to pilot and depress pilot button and hold. While you are holding button done push spark ignitor every few seconds until it lights. thank you and good luck

The thermostat probe on most residential water heaters is part of the gas valve. The thermostat is a non replaceable part of the gas vale and if your t-stat is bad you will need to replace the gas valve also.
This is generally not a very hard job just start off by shutting gas supply valve to off position.Disconnect main gas line to burner,line to pilot light, and thermocouple from gas valve. Remove pipe fitting from gas valve and use large pipe wrench to loosen gas valve.
Before you loosen gas valve you will need to shut water supply off and drain water from tank.MOST WATER HEATER GAS VALVES ARE PRETTY STANDARD ITEMS AVAILABLE AT MOST HARDWARE STORES. Just make sure you purchase valve for the type of fuel you have,such as l.p. or natural gas.Remove gas valve by turning counterclockwise. Use teflon tape or pipe joint compound on all threaded connections for reassembly. Hook up gas line,burner supply line,pilot and thermocouple lines. Refill tank and check and check for leaks. Light pilot and turn gas control to on. Set to desired heat setting . Also check all gas fitting for leaks. Good luck. Thanks

The first thing I would do is turn up temp control on gas valve.Control is located on front of gas valve at the bottom front of heater.They usually have a indicator dial on front with an arrow pointing direction.Turn dial to higher setting when burner is not on and this should turn burner on and provide hotter water. The control is normally turned clockwise to increase temperature.If control is already turned all the way up then water heater may need to be replaced.Depending on water quality in your area heater may have a large amount of mineral build up and it may not be capable of producing enough or hot enough water. If this the case all I can suggest is to try to drain tank and flush some of the deposits out. If you have installation manual it will give you instructions on how to do this. If not see if you have working shut off valve on cold water line ,if it works shut it off and connect drain hose to drain valve on bottom right side of gas valve. Put hose to floor drain or sump basin if you have one. Turn control knob on top of gas valve from on to pilot,this will leave pilot light on but prevent burner from working while draining. Open drain valve ,flow rate may be slow or not at all. Open hot water side of some faucet to provide air to help draining. You may try opening water supply valve to heater a few times to aid in draining. If you can get it to drain,shut drain valve off when done,turn cold water supply back on and shut off hot water outlet. Then when tank is full open hot water vavle to bleed air out of heater and piping. Turn control knob on top of gas valve back to on position. This should bring burner back on .It will take about 1/2 hour to heat. If you can't get it to drain or this doesn't help you might consider getting a new 40 gallon heater. Hope this helps. Thanks

Hello,
You may have a leaking gas valve control. Make up a squirt bottle of soapy water (use dishwasher soap and water) and spray the On-Off-Pilot knob for leaks, as well as the pilot button. Look for bubbles forming. Also check all the gas line fittings and connectors hooked up to the water heater for leaks. If you are smelling gas, do not attempt to relight the water heater. Close the shut-off valve on the gas line and see if the gas smell goes away. If it does, you may have to replace your gas valve. Depending on the age and condition of your water heater, it may be more cost effective to replace the control or buy a new water heater. Reliance is a common brand sold at stores like Lowe's. Typically, parts like your gas valve will usually only have a 1 year warranty. Check the manufacturer decal on the tank to see what their actual warranty period is. If you find a leak on the gas line itself, you will have to turn the gas off at the natural gas meter before disassembling the line to fix it. Use a soft setting teflon based pipe dope for the pipe threads. If you are uncomfortable doing the work yourself or don't know how to proceed, then call your local gas supplier for help. Douglas

Hello,Don't worry about the rust flakes as every burner collects then and is normal.The new control should click.Please check incoming gas pressure supply 3.5"WC natural gas / 9"WC for LP.Check it at the piolt tube with a pressure dial meter,I assume the water temp now is cold.Did you change the thermocouple also as this provides the power to run the control?

I would check to see if the switch on the blower pressure sensor is closing...When T-stat calls for flame, the circuit starts the blower, then the blower pressure sensor switch closes to allow the main gas valve to be powered.