If you seal the door shut in the right hand kick panel, that will prevent fresh air from coming into the cabin, it's path is to the fresh air vent located outside just below the right hand windshield wiper. I bought the gaskets for that from Doc Rebuild and it seals fine.
Really though, I never thought that door lead to any real problem if it's working and sealing properly, the one that would allow the most air in is the one in the plenium behind the A/C/Heater core.

There's another door located in the fresh air path accessable from the outside near the right hand wiper, if you look down the hole where the screen is you can see it. The vacuum line on my car was installed under the bracket pinching off the line, came from the factory like that. (no extra charge!). You can remove that from the outside, it's tight but not too bad.

If your car is like mine, look under your hood on top of the heater A/C box..............there should be a harness plugged into connector on the top of the box. Unplug the connector and you'll find 2 screws holding a resistor network to the box, remove them and remove the device. There should be two wire wound resistors as part of the device. Now look down the hole with a flashlight and you can see the door that lets all the air in. You can see if it's sealing flush and can at least look at the condition of the rubber.

I'll try to remember to take a pic when I get home.

Here is pic of connector to remove, look down inside and you'll see the door. You cannot acess the door without removing the heater/a/c box from the inside of the car.