Braindump in... 3... 2... 1... GO!

I like the idea of an "interview" (mock or otherwise) from a transitioned person that's integrated successfully into society as their real gender. Not a famous one, just an average person to show that it can be done - integration is not a pipe dream.
Extending on that.... reader voxpop style page. Think a forum style question, with lots of "readers" sending in their "viewpoints and experiances". Oh, and a question for "next issue", of course.
In the magazine / newsletter that I've read, there was also an "event calendar" for trans related events happening for the quarter.
Oh, there was also a review section for trans related books and films.
Perhaps some pieces written by family members or friends of people that have transitioned, and their road to acceptance? A way to tell the young readers that a) It's a transition for those around them too, b) Even if it takes time, most people accept you after a time, c) coming out is scary, but most of the time it works out ok.
Also, a letters to the editor section for feedback and comments regarding the last issues articles. It'd need a funky name instead of letters to the editor though... that's a bit Reader's Digest

.
Oh! An "Advice Please" column! (How could I almost forget that?! It's the staple of teen mags!) Where readers send in letters with a problem, and the "staff" give advice. It's good because the topics don't have to be unique - only the "situations" for the individuals

.
Maybe an article on therapy? Thing to talk about with your therapist if you get stuck, what to expect from therapy, etc. Young people would likely be looking at being in therapy (and nervous about opening up to a stranger) if they aren't already.
Names are also a big topic (I'd imagine) with the younger transitioner - getting your teachers to use a different name, picking a "good" name advice, etc.
I'd avoid going indepth on the topic of surgery, given the age group you're aiming it at (I know you didn't mention anything surgery related, it's just a thought).
There's so much content in passing and presenting - if you needed more padding you could always go "indepth" on a particular topic.
Look around at other trans newsletters, online and otherwise. I know FTM Australia do a PDF one you can download called Torque. It's not perfect, but you might get some ideas from it, anyway. The layout is terrible though, if I remember correctly.
Kudos for taking on an actual serious topic! I would have created the "Non Sequitur Segue", targeted the tinfoil hat brigade and gone for broke, personally!

(Aliens stealing celebrities used milk container lids to create army of robot dentists? You better believe it!

).