You can do two and three as many times as you want. In what ever order.
I suggest doing two first and review it.
After you review the diet plan, then I would do step 3 and then generate the cookbook.
I do not like the meal planner in the current release of SWAMI Xpress; so I never use it. But some people generate a new meal plan each week.
I do like the meal planner, in the soon to be released SWAMI Xpress 2.
If you health status changes or you find out one of your measurements is incorrect you can update your intake data and then regenerate the diet report.