It's not a problem man! This is something I've been interested in a while, and it's nice to see a shade-tree implementation of it. Practical physics and all that. I'd love to fiddle around with something similar if I had the time.
I'm not sure what your simulation includes, so I can't comment on the specifics, but there's a good general description of lean burn on page 5 of this pdf versus part load on page 2, where negative (pumping) work results from the difference in pressure between the crankcase and expanding cylinder after combustion that didn't take in the amount of fuel/air associated with full load.
http://www.researchgate.net/profile/...90ff65b52b.pdf
In terms of cooled EGR, I'm guessing that the when it's added, the pressure will start higher during compression, and maybe go a bit higher before combustion (1->2), the peak combustion temperature and pressure will be lower, and more work should be extracted from combustion, resulting in a lower 4 value and improved efficiency.
The addition of cooled EGR allows the specific heat of the intake charge to be higher, and the "effective" compression ratio, where "effective" describes how much stuff actually gets stuffed in the cylinder (since we aren't at stoich/normal pressure any more), instead of the volume ratio of expansion to compression, increases too. This allows for two avenues that increase efficiency (The efficiency part of cycle analysis is near the end of this wiki page).
Otto cycle - Wikipedia, the free encyclopedia