homonyms (they sound the same)

AKAIK, homonyms are words that sound and are spelled the same (but have different meaning). I'm pretty sure mixing them up in writing doesn't confuse anyone. Homophones are words that sound the same, but may be spelled differently (so, every homonym is a homophone, but not every homophone is a homonym). And homographs are words that are spelled the same, but may be pronounced differently. So, a pair of words that are both homographs and homophones of each other are also homonyms.

Now, I'm pretty sure that are tools out there that can parse text and have a basic semantic understanding of the text (which is necessary to be able to determine whether there's a problem with homo{graphs,phones}). But they may not be on CPAN -- it's far more likely they are available as ready-to-go applications. Perhaps you should inquire in a linguistics forum, they are likely to have far more expertise in this matter.