Dear Sabine,
a very interesting essay. The connections between theories reminded me of Sebastian de Haro's contribution to this contest---I think his framework could have a valuable application to your argument.
But I do have a couple of questions, if I may. First, can we not simply 'add' theories? Think of classical Newtonian gravity, and electromagnetism. Both have the same domain of applicability, but either could exist without the other, and they're not equivalent. So you could have a mass moving in a gravitational field, a charge moving in an electromagnetic field, and a massive charge moving in a combination of both fields. In the latter case, the predictions made using Newtonian gravitation would not suffice to calculate the object's motion, and similar with electromagnetism.
So it seems to me that to get an instance of 'strong' emergence, one would simply have to add a theory that postulates a 'charge' (in the general sense) which is linked to resolution, or size, or something like that; so the theory claimed fundamental no longer suffices to describe objects at a certain level, but no logical contradictions obtain---the fundamental theory simply isn't the complete description, just as Newtonian gravity isn't the complete description of the previous case.
An argument often made against such a case of strong emergence is related to Leibniz' 'principle of sufficient reason': there's no reason for additional charges such as the one I describe to suddenly emerge. But there's actually no difference to reductionism here: the fundamental facts that fix everything in a reductionist universe similarly lack further justification.
Of course, one could then turn the question around and ask what 'strong' emergence actually adds. And here, I'm afraid, there is no progress on the question of free will: whether my actions are determined by microscopic facts, or whether some macroscopic facts play into them, as well, doesn't change the deterministic nature of my actions. I would not be any more free if my behavior is determined by a law that cannot be smoothly extrapolated from a microscopic law---the question simply doesn't have any relevance to my freedom.
Indeed, the whole idea that it's physics that poses the greatest threat to free will is, in my opinion, already misguided. The problem is with the concept itself. As Schopenhauer has pointed out, "man can do what he wills, but he cannot will what he wills". What he alludes to here is that there'd be an infinite regress in arguing that the will could, in some way, be self-determined: in order to be free in my action, the cause of my action---my will, my desire to act---must be free; if not, if I am forced to desire something, and hence, act accordingly, then my action obviously wasn't free. But then, likewise, the cause of my will must be free---or else, see above. So the problem with the idea of free will really is that all my behaviors are governed by my desires; but I can't freely choose my desires (without collapsing into infinite regress).
That said, I do think there is a sensible notion of free will that can be salvaged; but that would take us entirely too far afield.