I did a little more sketching of sound change dependencies and desired ordering. I think what I'm missing is an example of how to document them. I think now it's time for me to look at Lexurgy.
Reading over the documentation, I think Lexurgy has most of the stuff I want, I just have to put in the effort to understand it, and get everything to line up with my current ideas.
I'll be doing that later, because I didn't get enough sleep last night, and I was tired all day, and I'm tired now. I'll have to try to fix that over the next few days.