General Comments:

In general I felt like I was unsure what the goal of each step was.  I was able to get a sense of the difficulties of each  step, but I think being more explicit in the goals of each step would help hook me.  

Specific Comments:

Section 4.1.1:

Paragraph 1, first sentence:  I think this sentence may be removable, though it's definitely a true statement!
Paragraph 1:
I think moving the third sentence to the front would help introduce the reader to the subject.  Maybe begin with something like:

"Our two goals are to find the relationship between the marginal totals and the available microdata and to find geographies that are synchronous with out current data."
Then you can say:  "In order to do this we need to match geographical IDs to one another."
Now you can list the difficulties in a couple of sentences:

1) One issue is the fact that we, more often than not, aggregate data from unharmonized sources
2) Same last sentence you have now, "The task ... through time."

Paragraph 3, Sentence 1:  The sentence is a bit long.  Perhaps you can end with "...by the character names."  I think the whole paragraph hold together without the aside about non-english speaking countries, but you could keep it in as a second sentence  as well.

Section 4.1.2

This section is about ecosystem generation, but the phrase is never used in the paragraph.  Which part is supposed to be the ecosystem generation?  Maybe you can define this explicitly at some point.

Paragraph 1, first sentence:  This sentence seems like scaffolding.  Mentioning the ability to work in parallel seems useful, but maybe you can put it at the end of the paragraph to stress that fact.

Last sentence beginning: "Our process then..."  This sentence is quite long, and I got a little lost in it.  It seems like the process you are describing is a series of steps, so maybe expanding to a numbered list would make clearer exactly what the steps are.  You could also split the sentence into a sentence for each piece.

Section 4.1.3

You also never use the word dissemination in this paragraph.  I think defining it will give the section more focus, and make it clear exactly what the goal of the dissemination step is.

Paragraph 1, last sentence:  I think this is the dissemination step, so maybe say that here.  I also think saying "We then" or "We can then" to emphasize that this step is the step after the one in the previous sentence, linking them together a bit better.

Section 4.1.4

I feel like an example would help here.  Either an example of the flexibility being helpful, or longer explanation of the different kinds of flexibility

Section 4.2

The first sentence takes a while to get to your main point, which is that you can do parallel computing.  Maybe you can begin with:
"Our method for generating synthetic populations is well suited for parallel computing".
Then you can add another sentence or two explaining why the method described in the previous sections implies that your method is easily parallelizable.

I like the example of exactly how many cores it is possible to use, but idk if the reader needs to know the breakdown of nodes and cores.  Maybe you can just say that the Olympus computing cluster has approximately 1500 nodes total.

Second paragraph

2nd sentence:  Can you add approximately before two minutes.  This statement distracted me and I started wondering if it could be exactly 2 minutes for every tract.

3rd sentence:  at the end "... to generate the entire United States."  Can you qualify what you mean here.  I think you mean to generate a synthetic population for the entire US, but I'm not sure.

Additional Comment:  You tell the reader how long it takes your current algorithm to do something, but if you also stressed how long it would take without parallel computing, I think it would make a stronger point.  (Also the number of minutes in a day is 1440, which is pretty close to the number of nodes you have access to, so your method basically turns days of computation into minutes, which is a cool comparison to make (100 days versus 100 minutes of computation).