What I would do if I were you is to call someone who does water damage repair and someone who can help with your water heater as well. This way it can be done correctly and efficiently. That would be my suggestion so that you can get your repairs done the right way. https://www.puroclean.com/services/water-damage-restoration/

Hello,
So you had water enter the burner combustion chamber through the access panel. That can be cleaned out, but was the gas control valve just above it on the water heater submerged under water as well? If so, do not use it or try to repair it. It is unsafe to use and the control must be replaced. Now whether or not it's worth while to replace just the gas control, depends on the age and condition of the water heater itself. Also, is this covered under your home owner's insurance policy? Damage from flooding is usually not covered in a standard policy,unless you had it added specifically. But it is covered if you had a water line break which resulted in the water damage. You should find out before you proceed with changing the control. We had the latter occur and our insurance co (State Farm) covered everything from clean-up to replacement). Hope that helps. Douglas