I am so glad you ask this question as this also bugs me and I would love to find a solid strategy that helps avoid all that re-work. Designs change. What you are doing sounds more complicated than what I am doing though.
Some strategies i have evolved for avoiding those problems follow. I'm not yet decided if they are good or not.
First, import important major external components that I will get sizing projections from. Then before doing anything else, create what I call "master layout sketches" at the top assembly level. These must be started first otherwise you can't take projections from them. These master sketches, typically 1 or 2, are never directly used to generate components. In those master layout sketches, design the whole layout with quite a bit of detail, as if I was working in 2D auto-cad. Some elements of the imported components (the bare minimum) will first be projected into these sketches. If done in enough detail and with enough dimensions, and parameters, and with ever-better predictions about what might need to change in future and drawing in allowances for that, and if you get constraints perfect (easier said then done) then you can later modify & control and update the whole design by simply editing those master sketches. Then when I create the rest of the components within the Fusion model, I always create a sketch under each new component and project details from the master sketches into the component sketch, then extrude from there and so on. I also try to avoid extruding from and to other component surfaces but instead extrude using projections and dimensions/parameters taken from the master sketches. One problem with this method though is that the masters sketches can some times become "broken" even though I exercised utmost caution getting sketches & constraints perfect. The result is the dreaded failed to compute error message when an updateable dimension won't update. Sometimes very hard to diagnose and fix - and when you do fix it, the reason it failed is sometimes related to some remote, barely connected line that you never would have expected would be the culprit.
I recently had a model where I had to replace a small slide buried in the heart of the design and I knew from experience it was going to totally wreck my overall design. For that I thought maybe a good way to approach it was to in a way reverse the design and assembly process until I got back into the "freed up" part to change so I could change it then roll the design forward again. This involved firstly suppressing or deleting some of the affected joints. Also temporarily tightly constrain angular motion on some of the pivotable joints so thing can move a bit but can not go berserk. Then change the component, preferably by only editing my master sketch and maybe selectively winding back the time line to delete stuff. Then roll time line forward repairing/deleting any thing in the time line that shows up as yellow or red, being damaged. And fully fix any yellow or red timeline items as soon as they appear. It still took me hours to resolve, but seemed to be a bit less painful than usual.
Also I find the as-built joints often fail and cause big problems, and they also can't be tweaked later, so I now avoid using them and only use regular rigid joints.
Also if what you are doing is very complex, you might want to consider using Inventor instead of Fusion - but $$$.
