Short of feeding them grade level articles to read about the statistical analysis of how literacy is affected by healthy nutrition and exercise habits, my thought, especially at the 6th grade level, would be to conduct an experiment. First, it would be difficult to call it a "literacy" test, as time likely does not permit an accurate measurement of each child's literacy, but for your purposes, maybe you could look at basic reading comprehension.
The basic idea would be that they read a series of short grade level pieces of text (you would have to find several that were similar enough in length and level for this to work) and take a basic comprehension quiz on each when they are finished. Perhaps they do one first thing in the morning, every morning. Though not perfect, it could be considered the control. Have them document what foods they ate the night before each reading quiz, and track their results in a chart. You might have them measure both how long it takes to read the text, and how well they do on the quiz at the end. You could conduct a similar experiment later with exercise/activity level rather than food as the variable factor.
I can't predict what kind of results you will get out of this experiment, and likely there is some detail work that might need to be looked at, but I imagine you could do this throughout a 4 or 6 week unit and have enough data to conduct some pretty interesting discussions. If nothing else, the class could look for patterns between types of food consumed and high or low scores. Additionally, you are going to pull in several inter-disciplinary skills (reading/comprehension, math, science, health, etc.) into one activity, which is always a bonus.