What is a decent way to organize a GUI that needs to show over a hundred items? [on hold]

Some co workers want me to make a very specified diff tool that compares two files. These files are very specific to another engineering program, but the structure of the file is exactly that of a csv file. However, the catch is one row in this file have around 250 fields (columns) and there can potentially be over 120 thousand rows of items.

While I can program a way to compare the two files, and eliminate rows of items that are exact, the problem I'm having is that I have no idea on how to display items that are different. What I originally have in mind is to create a GUI that shows the changes between the two files side by side (along with column name), but that sounds like a mess for the user to look at.

Is there a better design for this? Is a GUI even needed?