In my opinion the first one is correct as the applicant and instructor represent same person. Also for is better infront of two courses in my viewpoint.
The applicant is not the same person as the instructor. The instructor is the one who is writing on behalf of the applicant. The sentence is typical, for instance, for a letter of reference in which a teacher is recommending a student (the applicant) for advanced study.
Many thanks for your clarification. I reckon the decision of whether to use a singular or plural form here is based on the number of instructors rather than on that of courses. And after all the instructor for both courses is the same person. Got it.