The best place to start would be from the beginning. First, we assess people's comfort level and skill levels with the coding. Has anybody worked with json objects much? Who is good at the HTML formatting for character sheet? Does anybody have anything they feel they are particularily good at?
Second, we need to decide on how things work and get an overview of how things will work. I would say we take each action that needs to be done and walk through the steps to accomplish it. That will give an idea of what macros to have. For example, to set up characteristics: you have to access current values and display them, then you enter new values, save those values.
Third, where will variables be stored, what naming conventions to use, etc.
What are the opinions about multiple Lib files? Maybe one for combat, one for character sheet, and one for rules. Pros: better organization. Cons: more tokens to save, another source of confusion.
For properties on token, I say just have the base ones players would enter: str, dex, etc. The calculated values (aided, drained, damage, etc) would be handled with the set and getProperty functions. That way players cannot go and just change willy nilly and GMs wishing to customize the campaign file do not accidently break it by changing formulas or values that should not be changed. Plus it just looks cleaner.
I say put as much of the rolling on the character sheet as possible instead of macros to click. On the combat sheet you can have the hyperlinks that start and end your initiative. All stat rolls should just be hyperlinked like Brad has for skills now.
The macros for the player tokens should just call the main macro from the appropriate lib token. Again cuts down on accident changes breaking the file. I think it also might help with lag since instead of having to load multiple copies of macro files, you are just loading one.
These are just my thoughts. Ideas, thoughts suggestions? Brad, your input would be invaluable if anything I've suggested that you have already tried and found problematic.