terminology note: a "calorie" is a unit used in physics. The "Calorie" (nb. upper case C) is 1000 times greater, and is the unit used by nutritionists. I'm going to refer exclusively to the nutritional calorie, and not be a stickler for case sensitivity here.

If I were to do something similar, I'd make the basic accounting unit the "meal", and note that a typical adventuring lifestyle requires 3 full meals a day. Whether that's 3 sittings spread as breakfast, lunch, and dinner, or 2 sittings as water for breakfast and 1.5 "meals" at each of lunch and dinner doesn't matter. I'd go on to note that a sedentary lifestyle typical of craftsmen requires 2 meals (as can an adventurer on a "non-adventuring / downtime" day), and children can get by comfortably with one.

As for over/under eating...

http://www.weightlossresources.co.uk...lories_fat.htm says 3500 Calories is the equivalent of 1 lb of body fat. Eating 1000 calories too much over a month results in 30,000 extra calories, or 8.5 lb of extra body fat. It's probably simple to assume that each month of over-eating results in that much encumbrance. And if you are fat enough to drop an encumbrance level, you slow down.

I'm not sure, but I believe under-eating is covered by a subset of the fatigue rules in the DMG.