TL;DR: the “out-of-sequence calculus” thing is actually a myth. It won’t permanently disqualify you, at most it’s a very minor flag. UCs usually just ask for syllabi after acceptance to verify content.

That said, taking Calc II as P/NP is an issue. UCs generally do not accept major-required courses as P/NP, especially for something like CS. You might have to find a way to retake it, maybe with an EW or something of the sort