These files are about 400K each. One file has about 26,000 locations and the other is about 10,800 locations. At the rate it's processing it'll take me about 3.5 days on my PII 400 MHz.
I'll have to try your code, and see how much faster it'll run.
You should not have any trouble holding the full content of a 400KB file in memory. Read one whole file into an array, then run through that array for each line of the other file.