Character

As far as I know, the word for 'character' is 登場人物 (Tōjō jinbutsu).
1. Does it refer to all kinds of anime/manga/play/story/etc characters?
2. Can it also be used when talking about real life rather than art?
3. Is there a more commonly-used word with the same meaning?

I wrote this sentence:
あなたのクラナドの好きな登場人物が誰？ (Who is your favorite Clannad character?)
Any mistakes?

Thanks!

登場人物 is a compound of 'appear (on stage/screen/page)' and 'person' so it basically refers only to acted character roles.

I think キャラ is more commonly used for anime and manga characters. 登場人物 isn't wrong, but I think it's avoided just because it's a long word. Also perhaps because not all anime characters are people and it would be odd to refer to a character that isn't a person as 人物, even if it is in a compound word.

You don't need (or want) 'あなたの' in your sentence. If you're asking who is liked, it is obvious that you're referring to the listener.

クラナドの should be directly connected to 登場人物.

The particle after 登場人物 should be は ... I'm not certain if が is wrong or just a peculiar emphasis, but in any case は is normal there.

Favorite is 一番好き (lit. 'most liked')... 好き by itself just asks who you like.

The emphasis/most important information the questioner wants to convey is put before が or after は. The interrogative is the one in a question, so it's always put before が or after は.

誰が～ですか。
～は誰ですか。