Sidoh, I'd definitely take DEs and PDEs if I were you. First of all, they are extremely easy courses (at least at the undergraduate level, in most cases). So they shouldn't require very much of your time. Secondly, they are extremely important. They show up everywhere (including many areas of computer science), because they obviously describe so many situations.
The calculus you learned was also, most likely, geared towards application and away from abstraction and generality. But I assume you still liked aspects of the courses, and found them useful.