Hey,
I won a CGS last year going into my second year like you, and I was in the 5-16 months category... So you definitely qualify for the CGS. You are also not under any obligation to take 3 years to graduate in order to accept the CGS or the fellowship for that matter. When you have a defence date set, you just have to notify SSHRC of your intent to defend your thesis and they will end your scholarship for the next release of funds, which happens 3 times a year (September, January and May).
Best of luck!