I can do both of those examples. Syllables are a little hard, but I think the approach I've got in mind for metathesis should also work for syllables generally.

Rule feeding and bleeding is definitely hard. Something I'd kind of like to do is analyze rules and produce a graph that examines which rules interact with each other, and which rules are unordered with respect to one another.

Ultimately, this SCA is part of another system for hypothesis testing proposed reconstructions and sets of rules deriving child forms from them. The fact that it's usable by humans too is an added bonus. IMO, the most important contribution is that it can be used with a feature model, and understands (by default, though you can turn it off) that pʰ is different from p, and that a rule affecting the latter will not affect the former.