Since you don't say what you want different about the results, I couldn't modify it if I wanted to. In your sample, you show it outputting the reactants in the order E, C, A, B, and since that doesn't match the order from the file or alphabetical order, I have no idea what you're shooting for there.

I already did 99% of the work on spec. If you're trying to learn Perl, figuring out the last 1% will be good practice. If you're not interested in learning Perl, and just need a script written for your classroom, then again, I (and others here, I'm sure) will be glad to offer you a quote for the work.