Your propositions are all weird but not for the same reasons. First of all, we (French) would rather say something like “I peeled an apple, but not completely/entirely” (we do not like to reuse the same verb/adjective in a sentence).

Second, the tenses mean different things: if you say “J’ai épluché/pelé…”, it means that you were peeling that damn fruit but, somehow, it ended up not completely peeled. However, if you use “J’épluchais/pelais…” then it suggests that you had planned not to peel it completely and it sort of contradicts the use of “mais”, because there should be no opposition between the 2 parts of the sentence. So those sentences feel weirder.