I did some research on the yj heater systems and found this awesome write up... all credit to user "Wrangler Haven" from http://www.wranglerforum.com
I get asked a lot of questions about the YJ heating system and I've noticed a lot of posts on the forums about heater related issues. In fact, most people know very little about what exactly goes on inside the heating plenum when they slide those dash levers for heat or fresh air.
And because of this, diagnosing their own heater related problems can be difficult. So I've written up a tutorial on the basic heating and air functions of the Wrangler YJ.
So for those of you who have never been inside the plenum and want to know what's going on in there, read on:
Here is the basic layout of the YJ heating and fresh air ducts. For the most part the entire system is cable controlled except for the right side Cowl Gate which is operated by a vacuum motor. The vacuum is supplied by the engine and is switched automatically by the dash control panel. All other functions of the system are operated by cables controlled by the dash control panel. Each cable is directly connected to, and controls one function. All of the cables (except the Blend Gate cable) operate in one of two positions at all times to either open or close their respective gates.
The Blend Gate cable is the only multi-position cable and is used to mix warm and cold air within the plenum. (More on that later)
The blower motor is located directly behind and below the passenger vent (as shown) and pulls air directly from the cowl vent at all times while in operation. The blower motor operates only when the dash control is in the Defrost and Heat positions. It's speed is directly controlled by the fan speed switch on the dash control panel.
The Heater Core is located just to the left of the Blower Motor and has engine coolant circulating through it at all times while the engine is running.
Now lets take a look at airflow:
Here we have a picture of the heating system in the "Off" position. Notice the position of the dash control sliders. In this position, all Gates are closed, and the Blower Motor is not running. The Heater Core is always hot while the engine is running but no air is moving through the system.
Now we'll take a look at Defrost. In this position, vacuum is supplied to the vacuum motor which opens the right Cowl Gate.
This allows fresh air from outside to enter the system through the Cowl Vent and travel down to the blower motor. The passenger Vent Gate is closed directing the air towards the heater core. Notice the temperature slider has been moved over to the warm setting. This fully opens the Blend Gate allowing air to pass through the Heater core. The upper slider in the Defrost position opens the Defroster Gate directing the warm air upwards to the windshield dash vents. In this position the blower motor is running.
Moving the slider to the Heat position changes only one thing. The Defrost Gate closes directing air downward and out through the floor vents located above the transmission hump. The passenger vent gate is still closed and the blower motor is still running.
Moving the temperature slider to the center position moves the Blend Gate exactly halfway. This splits the cold airflow directing half through the heater core and bypassing the other half under the core. The bypassed cold air and the warm air from the heater core remix later and become moderate before being directed out of the system by the Defrost Gate.
Moving the slider into the Vent position does a number of things all at once. It shuts off the blower motor. It opens the passenger Vent Gate for the first time. And it opens the left Cowl Gate for the first time. The Defroster Gate remains unchanged and the Blend Gate (although it can be moved) serves no purpose since there is no airflow past the passenger Vent Gate. When this gate opens it blocks 99% of the airflow into the blower motor and the rest of the system.
The left Cowl Gate (the most difficult to see since it's deep within the dash above and behind the speedometer) allows fresh air directly into the cab bypassing the entire system.
It should also be noted that the right Cowl Gate defaults to the open position when the vacuum motor, which controls it, looses vacuum. This happens hours after the engine is shut down regardless of the dash slider positions. This typically is not a problem even in the rain as long as the Cowl drain tube remains clear. Should the drain tube become clogged, the Cowl can partially fill with water which can seep past both Cowl Gates. The Cowl drain tube is located within the engine compartment to the right of the battery.