Is there an upper limit on how many calories and protein the body can use per meal? If so, is it dependent on things like weight, activity before/after meal, etc.?

It is dependent on so many factors, it's hard to even fathom. There is plenty of research on this. Certain cultures consume all of their calories in one sitting and can take in easily 2000 calories at that one sitting and still appear to effectively utilize the intake. On the flipside, the "chanko" meal used by Sumo wrestlers allows them to consume relatively lower calories and still gain massive amounts of weight due to the timing and composition of the meal. Other people graze throughout the day. Some people have diet tied more to seasonal changes and become primarily vegetarian during certain parts of the year and then get the majority of their calories from meat the rest. What the research shows is that your body adapts to your current intake within just a few days - in other words, if you are eating low protein, your body will be ultra-efficient at using what little you get for tissue repair and recovery instead of energy. If you start eating high protein, your body will shift gears and suddenly become very efficient at using the protein for energy and less efficient at using it for tissue repair (but with more protein coming in, the net result is the same).

The thing with eating multiple meals is that anabolism/protein use does appear to occur throughout the day, so the multi-meal seems to favor a muscle building environment. The other catch is that blood sugar is related to energy and spreading the calories seems to stabilize this better, whereas consuming a huge meal can cause a sudden spike.

In fact, one study actually demonstrated that the risk of heart attack increased 350% after over-feeding, i.e. suddenly eating more calories than you are accustomed to at a single meal.

Jeremy