Well, This isn't the perl forum, so I probably shouldn't have posted that in here (my apologies). In Either language, though, I would read the first file, and compare it to each line of the second file. In perl, I'd read both into arrays, loop through and compare the arrays.
Attached Is How I would do this with a Perl Script. I'm working on doing it in bash shell right now also... but it seems a bit more complicated to me.... maybe I just like the feel of perl better, and so it flows more naturally and easy to me... but I'll keep giving it a go in Shell.