In Polish, you should negate the whole idea of 'liking you', not just 'you'.

What you wrote sounds like "It is not you who he likes".

They mean the same. "Cię" is the not-accented form, it definitely shouldn't be at the beginning of a sentence, and theoretically not at the end (but it definitely is in short sentences like "Kocham cię", "Nie lubię cię" etc.). "Ciebie" as the accented form, takes our attention, often shows some contrast. "Ona kocha ciebie" = "She loves you (and not Tom)".

In this sentence both should work. "On cię nie lubi" sounds neutrally, just a statement. "On ciebie nie lubi", at least to me, shows a contrast, a 'correction' of my views - I thougt he likes me, but it turns out, he doesn't.

Hm. „Ciebie” - you (singular), was (you plural), Pani/Pana/Państwa - you (showing respect). This is rather unidirectional translation, because of grammatical cases. If you want to translate from english, then you must determine which case to use: you (singular) -> ty, ciebie, tobie ...

Yes, it is. So "On was nie lubi" = He doesn't like you (referring to more than 1 person).