Well, Stage 3 isn't necessarily a "I was here for 5 years in a row" kind of thing. You can fluff it as being broken up over time, so if he went to the Academy and took OCS, you could fluff it as him having gone to the Academy, and then coming back later in life and taking OCS/Kensai Kami.
As for being a trainer, I'd probably just have him spend the points that are leftover at the end to get the skills that he wants from that. Or you could modify the University lifepath to make it a bit more military orientated.