If you want to have meaningful data, you'll have to run all the tests at the same air temperature, with the water starting at a consistent temperature and reaching a consistent temperature. I would suggest going just to 200 degrees on the water temp, since it's easy to read on any thermometer and avoids the subjectivity of just what is boiling and what is not. What i did was make a lid from aluminum flashing with a hole in it that my thermometer fit tight into, so I could leave the thermometer in the pot and hold it up off the bottom of the pot. A rubber band around the shaft of the thermometer ensured that it didn't ever slide down and touch the bottom.
Then you'll want to run several tests with each combination of pot and stove so you can average the results.
For my tastes, fuel efficiency is way more important than speed, but you can certainly record both for each test if you like.
Weighing your fuel is going to give you more useful data than trying to measure volume of fuel. For white gas, what I've done is to weight the fuel bottle with the pump in it before and after each burn. Likewise, with the canister you can weigh the canister before and after. I think I'd just leave the stove attached to the canister if it's an upright, so it's easier. For alcohol I guess you could weigh the stove with fuel in it before and after (I haven't run any tests on alcohol stoves).
I've done my testing in a garage with the garage door open - so plenty of ventilation and a concrete floor in case of spills, but out of the wind.
I'm looking forward to lots of nice data, please post all you get.