Joined: Sep 2006
Location: Montreal, Quebec, Canada
The heater system is actually fairly simple. It's just a fan blowing air through a mini-radiator (heater core) in your dash. The heat is provided by the hot coolant flowing through the heater core. So, if the engine is heating up just fine and the coolant is hot and the blower motor is blowing air, then the only thing left would be the flow of hot coolant through the heater core. If the flow is restricted you won't get enough heat exchanged to the air flowing through the outside of the heater core.
I'm not sure what sort of car you have, but changing the heater hoses on my 93 Sentra was a bit of a pain because the stock hoses are shaped to make the tight corners in the engine compartment, and, believe it or not, are different sizes on opposite ends of the same hose. I just bought a couple big chunks of hose and forced them to fit, but they are a bit kinked in places. Not an ideal solution. Removing the heater core is also a pain because you have to go throught the dash to get to it.
So my advice would be to get a Haynes manual and follow the procedures for the following: drain the coolant, flush the cooling system as per the instructions to clean out any scale or debris clogging small passageways, replace the radiator hoses and heater hoses with new ones (you can get the radiator hoses at any auto parts store, but I'd recommend just going to the dealer and getting the factory shaped heater hoses, it's easier and better, though more expensive), refill system with new long-life coolant and purge air from system. As a preventative measure you may also wish to replace your thermostat while you have the coolant drained and the hoses off.
With any luck all this may improve the coolant flow through your heater core and make the air come out hotter. If it doesn't work then you may have to replace the heater core, which isn't too hard but takes some time and patience. In any event, flushing your cooling system and repalacing your hoses is good maintenance and good insurance.