First of all, thanks from the detailed answer. One can always expect that from you :-)
Now, indexing may indeed be my way to go. In fact, I may be needing to do it in C++. I also ran indexing, it took 14 seconds on a 3e6 line file (the file itself is ~60MB) using STL streams and 8 seconds using C file access (fgets(), ftell()). The memory consumption is pretty good, only 12 MB for these 3e6 files (in a vector). Accessing random lines with fseek() is, as expected, almost immediate.
This closes in on acceptable, and I'm starting to believe that it is indeed possible to keep it in memory. (I don't need to handle files > 4 GB).
Another problem that I forgot to mention is that the file is being updated "live" and I should keep up with it. I can get notifications, and probably just add new indexes (the file always grows, never shrinks).
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