The "mother board" or integrated control module is essentially the brain that controls the sequence of operation in your gas fired furnace. It is located, generally, in the blower compartment. That is the bottom of the two compartments of the in the furnace. It looks like a circuit board with all the wires of the furnace leading to it.
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This could be due to a weak igniter which is not getting hot enough to ignite the gas, or the gas valve is not opening to allow gas to flow. First thing is verify if the gas valve is receiving 24 volts at the valve terminals, if not the board is bad, if it is receiving voltage the gas valve may be bad.
What kind of water heater do you have? In any case, it sound like a plumber should check out system.
Do you have indirect heater that gets heat from central heating boiler? Most indirect/boiler combo heaters have control that is set to heat the water first. If water is not getting heated, then the control needs repair.
Do you have gas water heater with gas central heating? The central heater may be drawing so much gas from meter, that other gas appliances are unable to function. larger gas meter or gas line may be needed. Or if furnace and water heater vent on same chimney, the backflow from central heat could be affecting burner on water heater especially if water heater has electronic sensor that stop combustion if air quality is bad. Venting problems can lead to CO poisoning, and are a serious matter.
Check for 24 volts across the two terminals on the gas valve when the ignitor glows. If yes, bad gas valve or blockage in the gas train. If no, bad ignitor or circuit board. Even if the ignitor glows, it still may be bad and not sending the proper signal to the board. If you jump the R and G terminals on the circuit board, does the fan still only run for 90 seconds? If so I would say replace the board.
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