BeGreen, here are some random thoughts about your experiment:
One of the main objects of this experiment (at least for me) is to see if using outside air keeps the remote rooms from getting cold. Therefore, I would get temperature measurements in various places around your home, from near the stove to the rooms farthest away, and on different floors if it is a multistory structure. The temperature measurements need to be made with and without outside air, and should probably last for at least an hour for each situation to allow time for the airflows and temperatures inside the house to equilibrate. You probably want to turn your regular furnace off during the tests so you can see just the effect of outside vs inside air with no heat sources other than the wood stove. To make any differences easier to see, you probably want to run your stove at moderately high heat and keep the burn constant, say by monitoring the stove temperature.
During the measurements, with and without outside air, I would try to control and keep constant all the important variables you can think of:
1) See that the temperature outside is approximately constant during the tests.
2) See that the wind is very low and stays that way, at least during your baseline cases. Later, if you want, you can run the experiment again when the wind is blowing at a constant rate.
3) Keep all the doors in the house in the same position and keep outside doors closed.
4) etc.
If you don't want to run around with a single thermometer to make the temperature measurements, you could just buy a number of inexpensive digital thermometers and put them in each place you want to measure. To avoid systematic errors, initially place all the thermometers together for awhile and see that they read the same temperature. If they don't, you can simply label the outliers with their temperature error and just account for that error when you make your reading. Almost surely the thermometers are all reasonably linear, even if their set points are a little off.
You might also rig up a poor man's manometer, a U-tube filled with colored water, and measure the pressure difference from inside to outside the house for each situation. Each mm of difference in water levels means a pressure difference of 9.8 Pascals. If your house is very leaky, like mine, I wouldn't expect much difference, but if your house is tight, you should probably see an effect.
A really good thing to measure and know is the actual air flow in the pipe which brings outside air to your stove. I'm not sure what the best, inexpensive way to make that measurement (anemometer, hot wire, etc.), but it would be worth looking into to resolve the debate in this forum.
Steve