Wow… from what I can gather that document has ~200 symbols with ~700 elements being instance of those symbols, and the document itself appears to have ~3500 elements. Yet I will say your document is very well organized .
The app is definitely spending most of the time doing symbol-related activities. It is funny how some operations (entering/exiting symbols) take forever (10-20 minutes), but in other cases the app is quite snappy.
I don’t know if I have great recommendations for this document. Avoiding symbols will be a performance benefit. But the document is still quite large. If you have individual pieces in separate .hype documents, you may find that you could create a “master” page using iframes/HTML Widgets instead so there isn’t a single Hype document that grows to be so large. Also if you can avoid too much nesting/grouping that may help a little.