Lets think some more. You have.
1. Changed the radiator
2. Changed the thermostat
3. Changed the heater core
4. Verified the heater control valve is working
5. Verified the blend door/actuator/motor, etc. is working
6. Verified the water pump is working
7. Checked all hoses for proper operation
8. Properly bled the system.
9. Performed cylinder leak down test with almost no leakage
10. Verified proper coolant level
Customer state’s that while driving down the road (at any speed) the heat will fade away and the air will blow cold for a short time. After replacing the first 3 items, the symptoms still persist, but are less prior to repair. You also mentioned that this happens around 50-60 mph. You also mentioned that the problem is occuring with the hvac in manual mode and not automatic climate control. Also you mentioned the engine temperature was perfect. Question:
1. Where you able to duplicate the problem?
2. Is the problem occuring at any speed or just highway speeds?
3. What is the temperature of the engine when the problem was occuring?
4. Does the temperature of the engine fluctuate at different speeds?
5. When the problem occurs, what is the temperature of the coolant going into the heater core?
6. When the problem occurs, does maximizing the heater control make a difference?
If you had a restriction inside the engine, I would think you would have some overheating issues. This problem seems to occur randomly, but there is a significant difference in air temperature when the problem occurs. The problem could be actuator/motor, blend door etc., but your customer has the settings on manual control (and already set at desired temperature) when the problem occurs. Since there is a significant change in air temperature, I am curious to know the temperature of the coolant going into the heater core when the problem occurs and also the engine temperature. So we need to find out the temperature of the coolant going into the heater core when the problem occurs (you could also check it during normal operation) and/or if there is even any coolant going in it at all during the problem.
If the coolant going into the core is low (during the problem), then maybe the thermostat is staying open, but if this is true, I would imagine your engine temperature should be decreasing as well. If the coolant going into the core is hot (during the problem), then you can verify hot coolant going into the core. Then check the heater core itself to see if it’s getting the coolant or getting restricted at the time of the problem. If there is a restriction, then why? Bad core, air possibly? If the core is hot as well, then the air should be hot. At this point maybe there is a motor/actuator, fan etc. problem.
There may not be any physical evidence that the water pump is failing, but maybe so? There maybe something on the inside going on that we can’t see or hear. Is the water pump providing adequate flow? Maybe at speeds of 50-60mph it’s sometimes having trouble pumping water to the core and possibly the rest of the engine, but then you said the problem happens at lower speeds as well. We could find out by monitoring the engine temperature when the problem is occuring.
Hope this helps.