At risk of being accused of being a Atlas-Thumper, I thought it might be useful to take a look at the thoughts of somebody a bit smarter than ourselves. 
From the appendex to ITOE:
AR: … the concept “existence,” at least the way I use it, is in a certain way close to the concept “universe” – all that which exists.
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Prof B: I would be completely satisfied on this if you could clarify one more thing for me, which is: why call the universe an entity, rather than simply a collection, since it doesn’t act as a whole?
AR: Well, you can’t really call it an entity in that sense. I don’t think the term applies. The universe is really the sum of everything that exists. It isn’t an entity in the sense in which you call a table, a chair, or a man an entity.
Actually, do you know what we can ascribe to the universe as such, apart from scientific discovery? Only those fundamentals that we can grasp about existence. Not in the sense of switching contexts and ascribing particular characteristics to the universe, but we can say: since everything possesses identity, the universe possesses identity. Since everything is finite, the universe is finite. But we can’t ascribe space or time or a lot of other things to the universe as a whole.
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I think one of the things that might be confusing here is this. Take the question, “is there a specific number of existents in the universe?” Well, first of all, we can’t count existents, but only entities. So switch the question to entities. (I make a point of stating this, because it’s a very different question, and some people have been equivocating.) One thing to notice is that this isn’t a very interesting question, in a sense. The universe is not a sum of all entities; it’s the sum of all existents. (In other words, it’s a metaphysical issue, not an epistemological one.) So even treating it as a strict sum, counting the number of entities in the universe, if you could, wouldn’t give you anything like a full understanding of the universe.
Ok, but take the question in reference to entities. Now here’s why I think somebody might think this is a valid question. Let’s say your room is the sum of all the entities that are in it, as well as those that make up its structure. So you count all the stuff in your room, and that’s the number of entities in your room. Obvious enough. Now you broaden the scope of the question: what’s the number of entities in your house? You go ahead and count all the stuff outside your room, you add it to the number of entities in your room, and there you have it. The idea might be that you could keep doing this until you’ve hit the whole universe, and then you’ve got a count.
There are a lot of problems here. Entities depend on a human perspective, and there’s often a contextual issue involved in what is considered as an autonomous entity. If you want to find out how much you’ve been smoking, you’ll consider each of the cigarettes in your ashtray as entities to be counted. If you want to clean your room, they’re just a pile of butts. Which is appropriate for counting entities? It’s totally optional.
That’s one problem. Another is, entities change. By the time you completed counting all the entities in your room, tons of entities elsewhere have changed into other entities, split, merged, whatever they do. Somebody dies in the next state over. Their body, over time, dissolves into its constituent chemicals. Now that one entity is a *whole bunch* of entities!
Plus, you’d have to assume you could count all the entities at a given time, at all. But how are you gonna apply a single standard of time to the entire universe at once?
Right, so I think that’s enough on that, but there’s plenty more to be said. (I’m not going to take the time.) Similar issues would apply to questions like “how large is the universe” – how large, measured from where? And how, when entities have a habit of *moving*, and it takes time for any method of measuring to occur?
Some other implications. DAC, you said that the universe is the sum of all matter and energy. That’s a big leap. How do you know that all there is, is matter and energy? One need not suggest, arbitrarily, that there *is* (or even possibly is) another form of existents in order to say that it’s inappropriate to define anything else out of existence. Another obvious implication is that RadCap is wrong in saying that the concept “universe” means the number of existents. In fact, the idea “number of existents” doesn’t make much sense. In what sense is the universe finite? Whatever it is, it’s that and nothing else.