You're confusing spelling (using the alphabet) with spelling (using hiragana/katakana). In Japanese, spelling IS the same as saying it.

きゆ and きゅ are pronounced differently because they're spelled differently (notice the size of the ゆ). Same goes for んあ and な.

I'm afraid I don't follow either. I meant that in Japanese spelling a word is just saying it, not anything about how words are romanized, etc.

That is, you say the word たに by saying た and then に, and you say the word たんい by saying たん and then い. Equivalently if you were to "spell" the word きゅう you'd say きゅ and then う -- you wouldn't say き・ゆ・う because that would be a different word.

(Incidentally na and n'a are not pronounced the same, as the previous example hopefully illustrates.)

I'm not aware of any words beginning with ん, it's usually placed between two other morae. If the following mora begins with a stop, it acts as a nasalization of that stop, similar to English n in "blank" vs. "bland". Otherwise, such as for んあ, it nasalizes the preceding vowel. E.g. the name 闇亞 (あんあ) is pronounced [ãa], whereas あな would be pronounced [ana].

I'm also not sure what you mean by kiyu and kyu, since きゆ and きゅ are clearly orthographically distinct.

This is coming more from having looked at Japanese in my phonolygy class than learning Japanese itself (although I have done the latter and noticed the distinction there as well) んあ is 2 syllables, な is one. This changes the prounounciation (most notably the length of the nasal stop.

Ki-yu (きゆ) and Kyu (きゅ) arr distinguised by the size of the ゆ character