Most refactoring is from the bottom up. Make the change easy, then make the easy change. I said "start a top down refactor" but redesigning from the top or all at once isn't really refactoring. Some of the actions look similar but you get few of the benefits of refactoring.
When the architecture problem has gotten away from you, or only becomes apparent late in the project, it's hard to see the trees for the forest. The only way to decompose the problem is to start somewhere and see what happens. With a top down rewrite the number of bits in flux becomes overwhelming, which is the anxiety I picked up from the previous commenter.
Mikado is just an exploratory development trick to help you find a way to make the change with refactoring. You try rewriting pieces until the number of concerns starts to multiply, you keep going essentially until your brain starts telling you, "this is nuts, you should stop", and you take that detail that broke the camel's back and do just that part, and build up and out from there.