The fact that the residual spectrum is uninteresting I totally acknowledge; that was admittedly an afterthought. I'm going to check out your hydrogenaudio link for details on how to better that section/figure.
As far as the fact that I only used MP3—that was kind of the point. I wanted to pick a seemingly low-hanging fruit so that I would have some nontrivial results to work with (i.e., cases where I could hear the difference). If I'd used high bitrate AAC and it was entirely transparent for my ears 100% of the time, I wouldn't be able to do much talk about false positives and hits and misses—talk which was ultimately the meat of the assignment, and thus of the article. The goal was, as I say in the "nota bene" at the top, not to say "Hey, look how unreliable MP3 128 is at being transparent," but rather to use MP3 128 to demonstrate the concepts of transparency and compression perceptibility.
As far as converting MP3 back to a WAV for ABX playback, I hadn't heard of that but I have to think that it would have made little to no effect for my test. I have a solid state hard drive so had no disk noise, and I did not hear the cpu fan on for either type of playback. It is something I'll consider for the future.
Again, I appreciate your feedback and thanks for taking the time to comment!