The biggest concern I would have is taking that input and being able to accurately normalize it. I can't see your files, but if you could normalize the data into proper table structures, you have a hope in using some sort of software available at your fingertips (maybe even Excel).
Sure you might not be able to do all your querying at once, but you could build your own MapReduce-like function from your tables.
As strange as this sounds, normalization is actually a non-issue. ANY problems with the data and all bets are off immediately, as it would mean we have a very serious problem.
hmm... aGAIN with the MapReduce. *sigh* I reckon I'ma gonna haveta go learn me that.