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If the heater core bypass refers to the water flow to the heater core, I would wonder why you did not flush the heater core as part of the system. You can drain water from engine, disconnect heater hoses and add a short hose to the heater and force a garden hose to flush the core.
I have not looked up the particulars for which heater system is on your car. Some just use duct-work to close off air flow through the heater core and the heater core always has hot water in it. Others will use a valve to shut off the water flow through the heater core and they can be either electric or vacuum operated. Combination systems are the third system which controls water flow and duct air flow at the same time.
Some of the Premium Climate control systems with Electronic displays have a computer diagnostic system which self-diagnoses problems but you need the sequence codes and explanation of where the bad part is located.
If they actually flushed the heater core itself you will need to check that the valve that allows coolant to flow through the heater core is operating properly. There should be a valve near the firewall where the 2 hoses attach to the heater core. In heat mode the valve should open and in A/C mode it should close. Please rate this answer, thanks.
these cars are infamous for coolant contamination cause restrictions in the heater core. i suggest performing a heater core flush followed by a complete cooling system flush. i have seen this dozens of times in these cars and this has been the fix nearly every time. good luck!
Sounds like the problem has to be the valve is not opening and thus not allowing the hot coolant to enter the heater coil. Manualy open the valve (engine firewall) and see if heat is present. If this works check your cable from the dash switch as it isn't working the valve properly and needs replacing.
Alternative 1: Blend Door actuator problem
There is a TSB out on this problem. If the thermostat and
everything else is good, you may have a problem with the Stratification
(Secondary) Temperature Blend Door. This door is now available separately
versus replacing the whole case assembly.The instrument panel needs to come off to gain access to it and this
might be a job best done by a Ford Dealer.
If you think you might want to give it a shot yourself, you
can get a copy of the TSB at the Ford Dealer. It is TSB number 02-23-6 dated 11/25/02. It has the repair procedure and
a list of parts needed.
Alternative 2: Heater Core needs to be flushed
Check heater core hoses.If both are hot, not enough heat inside, suspect blend door actuator.
If one hose hot and the other warm or cold, the heater core
need to be flushed (very common),