At the risk of stating the bleeping obvious, I would use a database for this. It's exactly the sort of task that most database engines are optimised for. While you might not want to store the data from run to run, even in this situation I would create a temporary database, populate it with the two files, and then use its query language to extract the data.
Regards,
John Davies
Comment on Re: Seeking guidance on how to approach a task
While a worthy reply, it ignores some real issues. Primarily, does the OP have easy access to a database? If so, does the OP understand how they work and does he know how to structure the query? If not, does the OP really want to go through the trouble of learning how they work to solve this one problem? etc.