So, I got the trade finder to run. Upon running it with only the first 150-ish items (out of about 3600), and only using amarr and jita as buy/sell systems, and only taking the top 10 results, it produced this:
As a sanity check I went to amarr and jita, found the real prices of the items and the quantities I would really buy, and got this:
As expected the quantities are pretty badly off, but the tool has successfully identified profitable trades and even put them in more or less the correct order. I'm calling this a win.