I think you really should consider using SQLite or MySQL again (like others have suggested in the comments). Most of the suggestions about pre-calculating indexes are already implemented "properly" in these SQL engines.
You said the speed wasn't good enough in SQL. Did you have the fields indexed properly? How were you querying the data? Where you using bulk queries, where you using prepared statements? Did the SQL process have enough ram to store it's indexes in RAM?
One thing you can possibly try to speed under the current algorithm is to load the (~100MB ?) file onto a RAM disc. No matter what you chose to do, either CVS or SQLite, this WILL help speed things up, especially if the hard drive seek time is your bottleneck.
You could possibly even read the whole file into PHP array's (assuming your computer has enough RAM for that). That would allow you to do your search via index ($big_array[$offset]) lookups.
Also one thing to keep in mind, PHP isn't exactly super fast at doing low level things fast. You might want to consider moving away from PHP in favor of C or C++.