It may be that a security clearance was a pre-enlistment qualification requirement for those with the expectation of attending Officer Candidate School.
I haven't been able to find out or figure out why 1965.
You found something else strange about his records. Why did he apply for the security clearance in Oct. 65? Anyone have a clue? Like stylin19a says, he was still at Yale.
His initial signature and date is on the last page. His signature appears in a 1966 security form too. He evidently wasn't in the Navy in 65, but his signature was witnessed by someone in the Navy.