Each character and position of every line of the first file has to be checked against each character and position of the second file.

What do you mean by "check" ? Most of my data processing work, when this involved, is done by dumping everything into an indexed MySQL or SQLite table and then running queries to do the dirty work.

Some top tier databases have ETL (extract, transform, load) tools that would allow you to simply specify the format of the two files and have it automatically load them for you.