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You also need to connect a new flexible gas line to the pilot box. To create a tight seal, spread Teflon dope (a putty suitable for gas line connections) over the fitting. After threading the fitting into the pilot box, tighten using the open-end wrench. Remove the old fitting on the incoming gas supply with a pair of pipe wrenches. With another layer of Teflon dope, tighten a new fitting on the gas supply.
To connect the water heater to the water supply you must transition the water valve removed earlier. Start by cutting off the old fittings with a pipe cutter. Then, burnish the cut ends with an emery cloth to expose fresh copper. To prepare for soldering, brush on a paste flux (Image 1) and twist on a copper union with built-in solder. Continue joining segments of pipe with unions and two new fittings in this manner. Once the correct assembly is achieved, solder using a propane torch to apply even heat to each union liquefying the solder to make a seal (Image 2).
With the new valve assembly ready to go, roll Teflon tape over the new fitting and counter-torques with open-end wrenches to connect it to the cold-water flex pipe installed earlier. Then solder a new union between the valve assembly and the incoming supply pipe (Image 3).
With the cold water supply connected, turn your attention to the hot water side. Start by soldering a new fitting to the outgoing pipe that was cut earlier (Image 4). After rolling on some Teflon tape, connect the hot flex pipe. You're now able to fill the heater with water. Turn on the main water, and then the cold-water valve. While the water is filling, connect the gas flex-line (Image 5) and reattach the duct and draft hood to vent the heater.
Once the water is completely filled, open the gas shut-off valve and ignite the pilot light, set the temperature, and the heater is ready to use.