NTLK is an interesting toolkit which allows building NLP-based applications. This can be used for practical applications which require for example POS tagging, or which implement simple classifiers or entity extractors.
I'm unsure of what a "language understander" application would encompass, however, but this sounds like something which may be beyond what can [easily] be based upon NLTK.
Reading the question completely, and its reference to morphophonics, seems to confirm that NLTK would probably not serve the OP's purpose very well; to my knowledge NTLK doesn't offer modules that deal with text at this level. You may want to check this for yourself however, as NLTK is a broad and active project and may have seen recent additions in this area.
