Now that we've got a list of points that are "dense" enough to spawn structure and some information about how much matter and energy they contain as well as their history, how do we use that information to introduce structure into the local area? This will take me back to what I mentioned earlier about chemistry and fusion of elements. In essence what we have is a whole lot of Element 1 contained in a very small area. We need to take that homogenous soup and turn it into a physical object.
Step 1: We have to determine, based upon the properties and history of that area, what new elements will form there and how much energy it will take to form them—the idea here being that eventually we will run out of energy to form new elements. The stage/rate at which this happens will produce certain attributes of the eventual structure. The initial density of the area will have a lot to say about that, since a higher density will form heavier elements with less wasted energy.
Step 2: Based upon the elements resulting from Step 1, we determine what sorts of chemical bonding will take place and in what amounts. This refers back to the simple chemistry developed earlier—certain elements will bond with others.
Step 3: The resulting substances from Step 2 will give us an idea of the nature of the structure in question, its chemical composition, size, etc.
One of the biggest kinks to work out here is in the chemistry. Likely I will need to go back and add some more sophistication to that system so that, while elements with the proper "numbers" will bond with certain others, there needs to be some preference in their bonding so that elements will bond in a path-of-least-resistance sort of way.