When the air handler is only used for heating, they often don't have a fan-only control.  That's a problem for setting up the house in worst case conditions for combustion safety because the leaks in the ducting, etc. can really impact the house pressures.  Some furnaces have a control on the high limit switch that can be used to turn the blower on.  But if that's not available my strategy has been to set the water heater up in conditions as bad as possible and test it for spillage, etc. and then fire up the air handler, quickly check for spillage, run upstairs and set up the doors, then recheck the water heater and the furnace.  Does this sound familiar and reasonable?  Alternatively you could ignore the "lowest BTU appliance first" rule and start with the furnace.

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