Heater intermittently cold?

If I had to guess I would say probably the heater core is partially plugged. Would need top back flush it and will probably see a lot of dirty stuff come out.

Likely there is air trapped in the block. Did you follow the V6 coolant refill procedure? The V6 and DOHC motor WILL overheat unless all of the air is removed from the coolant system. The procedure must be followed completely and each step is important.

V6 3.8 Coolant refilling procedure

Filling — 3.8L

CAUTION: Some vehicle cooling systems are filled with Motorcraft Premium Engine Coolant VC-4-A (in Oregon VC-5, in Canada CXC-10) or equivalent meeting Ford specification ESE-M97B44-A (green color). Others are filled with Motorcraft Premium Gold Engine Coolant VC-7-A (in Oregon VC-7-B) or equivalent meeting Ford specification WSS-M97B51-A1 (yellow color). Always fill the cooling system with the same coolant that is present in the system. Do not mix coolant types.

CAUTION: Engine coolant provides freeze protection, boil protection, cooling efficiency, and corrosion protection to the engine and cooling components. In order to obtain these protections, the engine coolant must be maintained at the correct concentration and fluid level in the degas bottle.
When adding engine coolant, use a 50/50 mixture of engine coolant and clean, drinkable water.
To maintain the integrity of the coolant and the cooling system:

NOTE: The addition of Motorcraft Cooling System Stop Leak Pellets, VC-6, darkens Motorcraft Premium Gold Engine Coolant from yellow to golden tan.
Add Motorcraft Premium Engine Coolant VC-4-A (in Oregon VC-5, in Canada CXC-10) or equivalent meeting Ford specification ESE-M97B44-A (green color), or Motorcraft Premium Gold Engine Coolant VC-7-A (in Oregon VC-7-B) or equivalent meeting Ford specification WSS-M97B51-A1 (yellow color). Use the same coolant that was drained from the cooling system. Do not mix coolant types.

Do not add/mix orange-colored Motorcraft Speciality Orange Engine Coolant VC-2 or equivalent meeting Ford specification WSS-M97B44-D. Mixing coolants may degrade the coolant's corrosion protection.
Do not add alcohol, methanol, or brine, or any engine coolants mixed with alcohol or methanol antifreeze. These can cause engine damage from overheating or freezing.

Do not mix with recycled coolant unless it meets the requirements of Ford specification ESE-M97B44-A or WSS-M97B51-A1. Not all coolant recycling processes meet these Ford specifications. Use of such coolants can harm the engine and cooling system components.

Place the heater temperature selector in the maximum heat position.

CAUTION: On 3.8L engines, the vent plug must be removed before radiator fill or the engine may not fill completely.

NOTE: It is important to maintain engine coolant concentrate between 40 percent or -24°C (-11°F) and 60 percent or -52°C (-62°F).

Fill the engine cooling system with 50/50 mixture of water and engine coolant.

After filling the engine cooling system, add coolant to the vent until full. Install the vent plug.

Leave the pressure relief cap off and run the engine until it reaches normal operating temperature.

Stop the engine and add the correct engine coolant mixture to the degas bottle/coolant expansion tank until the coolant level is between the COOLANT FILL LEVEL marks.

Turn the engine off and allow the cooling system to cool. Check the level in the degas bottle/coolant expansion tank, and add a 50/50 mix as needed.

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Never run the motor with the vent plug open as this will draw air into the system making the job HARDER.

Note the steps about allowing the motor to cool. This is important.

Note, if the heater suddenly STOPS working, this is a sign there is air trapped in the system. Don't ignore this symptom.

Flush the system and use Preston from your local autoparts store. Can't go wrong.

Don't use Dexcool.

bump, where the eff is the vent plug? This is different from the drain ****, yes? pic requested

EDIT: apparently C o c k is a dirty word, even when preceded by "drain" LOL

Yeah the procedures sound confusing slightly. Even I cannot leave the radiator cap off while the engine warms up. It just goes to show, as the coolant in the engine warms up , it expands,, thereby creating pressure down the lower water pump hose to radiator and thus eventually making the coolant spill out the radiator cap. On slightly newer models, such as yours, there is no cap on the radiator. Instead you have a "Degas bottle" on the side. I would assume the same thing would happen with this. The degas bottle is pressurized like the rest of the cooling system. It's not simply an overflow bottle. So to sum it all up, just because the coolant level has risen in the tank, don't mean the T-stat is open. To tell you the truth, the only way I know of to verify the T-stat has opened is to check the upper radiator hose and see if it got hot. It it is, the t-stat is open.

@ badmutha - And to answer your question if needed.. or FYI to anyone else...
The vent plug will be on top of a small metal pipe piece with a temp sensor protruding from the side. It will also have a larger white cap attached to it with words similar to " Replace before running engine - Remove with engine off while filling" .... or something along those lines.