I've worked in digital marketing since 1997, led business operations at two digital marketing agencies, and advise digital agency owners on improving the business side of their agencies.
Agencies tend to use some version of the standard consulting phases: Discovery, Analysis, Recommendations, and Implementation. Some agencies like to give them cutesy, proprietary-sounding names. In my experience, I'm not sure that really fools anyone.
You also want to convey that you understand their problem. When I evaluate proposals by agencies, the biggest problem is talking about the agency and not the client. Focus on how they'll benefit (including likely metrics and potential results), not what you'll do.
Milestones and deliverables will depend on the nature of the project. If it's implementation work, you might list typical deliverables (e.g., landing pages, nurture campaigns, or eBooks). If it's strategy work, your deliverables will be the research, analysis, and meetings you do to make recommendations. Beware of getting too specific about granular deliverables -- you don't want to prescribe a solution before you [get paid to] diagnose the problem.
Which leads to your second point -- don't give them the plan/strategy you have in mind until they pay for your help. Don't treat your strategy advice like the free coathangers at the drycleaner (so value-less that they're thrown in with your cleaned shirt).
Many prospects won't like this. I think you should refuse to do business with them. When agencies deliver spec work (a la 1960s ad agency pitches from "Mad Men"), they're making it harder for everyone else (and themselves), by showing prospects and clients that strategy has so little value, you're willing to give it away.
What can you do instead? Position yourself as an expert as solving their problems in their industry niche. (If you call yourself a "full service agency," you're already doing it wrong.) People hire specialists. If you need heart surgery, would you hire the surgeon who does general heart surgery or who's done your specific procedure 500 times? I know I'd pick the specialist-specialist!
Instead of sharing specific recommendations, use case studies of how you've solved similar problems for similar clients before. And if you don't have similar clients yet, use the closest analogy you can. You've got to start somewhere. And it's a reminder about doing the same type of work over and over again, rather than jumping around to a million types of projects.
Ultimately, don't over-invest in the proposal process. Once it becomes clear someone isn't a good match, gracefully bow out and invest your energies in working with clients who value your expertise by paying for it.
Good luck on your proposals! I'm glad to do a call to answer any followup questions.