We traveled by train in Europe once and we saw nothing! The train was either in a ditch , behind a wall or a hedge. Nope, rent a car, get a map and see the country, stay at small hotels in small towns and you meet people. Ask those people where to eat and what to see and you have an adventure not just a guide book experience.
You are 1/4 right. What you have to do is first get a map of Europe. Then plan where you want to go. All those cities from south to north and back. This is done in advance, not off the cuff. It takes planning. As to how much time you wish to spend in each city or country. Then create a schedule. Then find the train schedule from point-to-point. And the ferry schedules too, depending upon which countries you want to travel between and from where. Then you can get on the net now and reserve hotels or bed-and breakfasts for your arrival times in all those places you choose.
You have limited time in each place like this, so you use it the best. And you have a chance to meet people that live away from big cities and see how they are doing. They will enjoy your interest to talk and meet.
I had the pleasure of seeing everything between Alicante, Spain and Dunvegan, Scotland and come back in a month. Just nice people. And we travelled through 9 countries. Fast. No aircraft. And not much rest.
And First Classe trains and ferries because we planned it months before doing it! Try it:)