I take pretty much the same approach as Ben H, and also have a spreadsheet to calculate efficiency.
Like Ben, I assume a constant burn rate, and agree with him that this gives a pessimistic figure.
I calculated the lower heating value from bond enthalpies for ethanol and methanol, since published figures vary. As do those for bond enthalpies… I used LHV, since, although some water of combustion does condense on the pan at the start of heating, by the time the water has boiled, this condensation has evaporated again, and is lost to the system; it's not a condensing system…
I allow the volume and temperature of the water to be entered, and the weight and type of the pan, and the fuel type, volume and temperature. So I account for heating and evaporation of the fuel, and the heating of the pan and water. I don't account for the heat of vaporisation of any steam given off during the boiling phase, but this is generally small.
I measure the time to boil, and the total burn time. These two figures, along with the water and fuel volume, are the fundamental ones to determine efficiency.
I always test with a lid in place, and determine boiling point as when steam is emitted as a decent stream (under some pressure), rather than mere wisps.
I'm at about 70m ASL, so altitude and pressure isn't an issue.