Hi Andrew! I am actually in almost the same situation. While the process is fairly clear-cut for RegForce members, it isn't so clear for reservists. Especially in terms of going on course, whereas your unit is aware and there is no issue, going on course means you'll be working with a whole different chain of command and group of people. And that could be great, or bad, depending on who you work with. That's partly why I opted not to go on course and find a Class B instead for the summer. You've got guts!
Like you said, everyone is extremely understanding, but aren't exactly sure of the policies/how to handle gender segregation. I'm starting to believe that the information just isn't out there, and the best way to learn is by talking to those who have been through it before you (that's the tricky part!). But I'm sure you're aware that what works for others might not work for your or your course situation. Throughout my coming out, I was lucky enough to meet a few others that were ahead of me in transition, but I still had to figure out most of it on my own. Luckily my unit was on board and very helpful (where they could be).
The bathroom/showers dilemna, that's a huge one (well just like anywhere else in society) but it is especially more of a problem on course. Really, how many jobs do you know of that require you to shower with your coworkers? Essentially, you have to figure out what works for you, what you're comfortable with, and what options are available to you. Hence why you need to notify your chain of command. In the past, I know they have allowed FtM's to use separate washrooms (Ie. go up the road where single stall showers are available) instead of forcing them to chose between one or the other. However, if you have to pick one, the choice is yours. Ever heard of the rule "when in doubt, use the women's washroom"? When in doubt about your safety, usually the women's washroom is the best bet. Yeah, that sucks, I'm not a big fan either, and it goes against everything you've been working towards, but you do what you have to do right? Another advantage of the women's washroom is that it is MUCH less crowded, and odds are it might be near-deserted in most cases. It would also be easier to explain the situation to a few women on your course, so that you can shower in peace, as opposed to outing yourself to 95% of your course (men).
As for bedspace assignments, I haven't encountered that problem yet, but I've given it a lot of thought. On exercises, everyone is thrown in the same tent/building, female or male. Wonderful isn't it? As for course where they strictly enforce male and female quarters, I would assume that they would try to put you in whatever quarters matches the legal gender identification on your course information. If...
a) You have an "M" on your liscence, then you shouldn't have issues, they'll throw you in with the other boys, and problem solved and smile!
b) You still have an "F" on your driver's license, then I'd suggest talking to whoever is in charge of assigning rooms, and see if you can be switched. It is a grey area, it all depends on who you talk to. As always, you might have to educate a few people on the situation to get your point across.
I've had many people ask me the same questions, I asked the questions, and I still don't have definite answers. Like I said, I am under the impression that since transitioning is such a grey area (with many, many shades of grey), that you need to find out what works for specific situations, and hopefully, that they would be willing to bend the rules of gender segregation. But that's just my impression, I guess we'll find out soon enough!