Punctuation inside or outside quotations?

I would be grateful if you could tell me if I punctuated the following sentence correctly:

Plag (2003: 5) argues that such cases are “rather annoying”, and “[t]he notion of what a word is, should, after all, not depend on the fancies of individual writers or the arbitrariness of the English spelling system.”

(I put the full stop inside the quotation mark at the end beacuse the sentence is complete in the original text)

Here is the original text:

For our problem ofdefining what a word is, such cases are rather annoying. The notion ofwhat a word is, should, after all, not depend on the fancies ofindi vidual writers or the arbitrariness ofthe English spelling system.