1.) Ideally you would using dependencies to sequence the project and avoid manually setting the dates. If you shift out the start/due date of the project it would impact all of your milestones. I would hop on one of our Q&A webinars to see this in action and deep dive into scheduling (http://webinars.clarizen.com).
2.) That depends on whether or not the milestones are usually the same from one project to another. If so, I would templatize the project, otherwise I would go with the milestones.
3.) For the calendar you can use the ical integration, a roadmap view, or gantt charts. As for the report, if your milestones all have the same name (or you set a field like milestone type the same for each type of milestone) you can easily create a report for this. You can also use the Milestones or Work Items pages to view this data in a report-like interactive view.