My plan to quantify crop output is basically to use different crops for each test plot. I'll also have to either make note of how much of each crop I have before starting the experiment and just look for the difference, or just flat out process everything before beginning. I'll also have to give my threshers, brewers, and cooks a break while doing this so that they don't mess with the numbers.
I'm also planning to leave the fields fallow the season before the experiment so that there aren't any old seeds carrying over into the experimental period. Come to think of it, the fields should probably be left fallow the season afterwards to give the dwarves the chance to harvest everything that was planted during the growing season. Once the final harvest comes in, I'll take a look at the stocks.
As for having enough seeds, that issue is probably a good reason to flat out process all the crops before starting. My seed cap per crop is 200 I think, so as long as the test plots aren't too big I shouldn't run into problems with running out of seeds mid-test, especially since it looks like I'll be doing this test with dabbling planters. That being said, if I ever get the notification that a planter has run out of seeds during the test period then I'm going to have to restart the experiment.
I do have one question that's important to the experiment. I know that a higher planter skill is associated with faster grow times and larger stack sizes upon harvesting. What I need to know though is if different crops have different base growing times and if some are prone to larger stack sizes than others. If they're all the same then I can get away with my plan to use different crops all at once during a season, but if not then I'm going to need to space out the experiments so that I don't run into the problem of trying to figure out which plump helmets came from which plot.