I would suggest something more emperical. You're not going to get a very accurate evaporation figure for your short term test using a complex method that will likely require a number of assumptions, and it sounds like accuracy is fairly important. I spent some time trying to design an evaporation pond for disposal of potentially contaminated water a couple of years ago and ran into this same issue. We ended up going a different direction because of the environmental conditions of the area, but I did figure some things out with regards to evaporation rates.
If you're already doing field measurements, you might as well measure the evaporation as well. Get yourself a standard Evaporation Pan. They're basically big flat pans that you set outside. They're straightforward, in that you put water in, measure the depth, wait, and then measure the depth again. You obviously have to account for rain and things that may happen during the test. Set it up and run the evaporation test at the same time as your other test and you'll have a more accurate number for evaporation in the very specific conditions of your test than you'll get trying to calculate an estimate from multiple variables.
Note that the evaporation rate from a large body is less than from an evaporation pan. The body of the pan heats up and contributes to evaporation. There's a reasonable amount of literature about scaling factors to go from pans to lakes, though, and you should be able to come up with a good value. My notes say that 0.7 is commonly used for many applications, but you might be able to come up with a better value for your specific case. The term you'd want to look up is 'Pan Coefficient'