I'm flattered that I've got quite a few replies on the subject now. I'm sorry that I've taken a while to reply to everyone. What has been said is all very useful, and your perspectives have given me some hints as to which areas I need to tweak or reconsider.
I'll address you in turn.
First, Shanami:
I wrote a whole paragraph on Chimata no kami until Yasuhei pointed out that a lot of gods and goddesses in fandom behave like the AMG series deities. So as an answer, no; they aren't concrete entities and they do not have physical bodies. I have to admit that I have tweaked the chimata no kami to be a dichotomous entity, male and female, from the original single male god. Since they share a shrine, and some amount of their power, a yang leaning imbalance will tilt things in his favour, give him more autonomy over her. I suppose they are more like the anthropomorphic personifications of some fantasy novels, whose identity and form change dependant upon the faith and attention of mortals.
Regarding your questions about high school and marriage, I dealt with those in the clearly labelled "Setting" paragraph at the top of my first post. You can take "life has continued as usual" to mean that their engagement continues and they have not yet married.
Regarding the plot direction, I am not certain how the final character conflict will out. I wanted to be more sure of Ranma and Akane's canon gender related issues before I cemented anything in. But I thought that in my original post I was being clear enough when I said that the goddess
claims that her husband is the source of the imbalance, and that Akane needs rescuing. I haven't nutted out the full nature of the god and goddess' duplicity, but there is supposed to be something fishy about this whole premise. I'm glad that you picked up on that.
My final direction isn't both of them exploring the feminine, but both of them learning to explore the whole and all. That will involve the feminine, absolutely, but I'm just as frustrated with hyper-feminised Ranma fics as I am with hyper-masculine, and it's partly why I wanted to write this in the first place.
Next, Spokavriel:
Ah! I realised my large mistake. In the uni research I've done in the last few years, when we say "chemical 1 has leeched out of the bone", we mean to say that the chemical has left the bone and entered the surrounding soil or other material. I used that phrase without thinking, and it's probably caused more confusion than my original flubbed post. So Akane's becoming steeped IN yan, not drained of it.
Please forgive me for a very stupid mistake like that.
So it's a little redundant, this next response of mine. But as Ranma's female form isn't enough to create a yin imbalance - he's man through and through conceptually - any similar attempt to exert magical physical changes would have no effect on Akane.
I hadn't thought about the option of a spiritual healer becoming involved. I don't want to make the scope of the story too large, but it sounds like something I should at least consider.
I also haven't thought about involving too much of the ensemble cast. I intended for Ranma to avoid Nodoka for a lot of the early story, in an attempt to hide her experiments with yin. But since Nodoka and Genma have handed down some of their issues to their son, it would make sense to involve them in the core story somehow. I'll have to do a bit more thinking about how I might fit that into my concept, but it could quite possibly make for a much better fic.
And finally mondu_the_fat:
However, when gods themselves come into play, the author is saying "THIS is how its supposed to BE!"
I honestly don't mean for the god and goddess in this fic to be dictating the evolution of the characters, or preaching to the readers. I do not mean to re-inforce the dichotomous and restricted concepts of gender and sexual identity that Genma and Nodoka endorse in the manga at all. In fact, I wanted to write a story that showed Ranma and Akane confronting these concepts that they've learnt from their parents, and moving past them.
I don't think that I've receieved a comment for any fic or idea before along the lines of "politically incorrect". Since I'm a bit shocked to see them there, I'd like to ask you to elaborate on what pinged your PC radar when you read my post. (I'm worried that I'm coming across here as defensive or narky. I'm not, honest! I'm really curious, and quite eager to hear more from you on this. Blast the internet for lacking visual and audial context for sentences!)
I'm also concerned that you're seeing too much of the canon "man amongst men" in my spiel where I did not intend there to be any. I wanted to show Ranma gaining new perspectives on his identity, and moving beyond the, as you say "man amongst men" ideology.
I'm actually doing my best to avoid an "author tract". I'm not sure whether you meant that the regaining of spiritual balance and Taoist themes was going to be my tract, or the gender identity exploration. So it'd be useful to me if you clarified that, too. To be honest, I wanted to write this story for the sake of the story that it could be. I have no designs on promoting my own take on sexuality, or shoving in any preachy themes. So if you could clarify exactly what you meant by "author tract" and perhaps which paragraphs specifically made you feel concerned about this, I'd be in your debt. If you could point out my "man amongst men" sentences or passages, too, that would be wonderful.
-- Thank you all for responding! I got feedback that I wasn't quite expecting, which means that I'm really grateful to all of you; you've exposed some gaps in my concepts and planning. My fic is going to be much better, and most of you have taken the time to write much more in-depth posts than I'm used to expecting. It is, like I said above, very flattering.
I hope that some of the clarifications (and apologies) I've made resolve those questions. I'd like to hear more from you, especially mondu, if you have the time.