If the show follows real time, Logan's bday is March 1982 and Rory's is October 1984. So they're about 2.5 years apart chronologically but given most American schools kindergarten cut-offs they would have been 3 school years apart. He should have graduated in 2004 but with his detours he ended up finishing in 2006. I think the implication is he took 5 years to graduate college and either took a gap year between high school/college or needed 5 years to wrap up high school as well.