I was watching an interesting tv program about human development and Pf. Brian Cox said something very true: that Science is just asking simple questions and observing small regularities until we have a pattern, an intellectual framework by which we can answer the larger questions. That the 'how does it work' comes before the 'why does it work'.
I think that's where homeopathy is at - we still have to know how it works before we can build a model of why it works. We know that homeopathy changes us in regular ways - certain remedies in certain ways and others in other. The singularities of successful healing don't matter until we find the regular pattern that is common to both successful and unsuccessful attempts at healing with these potencies.
One pattern is the aggravation - I've never seen an energy medicine work without at least a few minutes to a half an hour of an absorbing or rejecting aggravation.
Another common pattern is the vibration - I can feel the pills vibrating on my tongue spreading through my body. I have seen very weak dogs bodies vibrate entirely with a high dose of Tuberculinum, especially when it is too much to absorb all at once (not the right way to heal).
Another pattern is the change - it changes the being in some new direction, for better or worse.
Beyond this we need the materia medica to understand how the remedy works in a normal body as opposed to what it does in our particular instance of usage. More later.