As you are starting a Ph. D. you will realise that you have to become not only THE world expert in your particular topic but also an expert in all the surrounding areas. The viva voce exam can throw really nasty curved balls at you...
So what I am trying to say is that you really have to understand the history - how and why the current situation developed in the railway industry, how has the economic, technical, social and political framework in which the railways operate changed. And how these are likely to change in the future - certainly within the timespan of your study. Only then will you be able, in my opinion, to properly scope the different challenges and get some idea of their relative importance.
If I were you I would try to find some good sources (preferably academic, but there are some good general books) giving a 'tour d'horizon' of the main periods of development - the early railways and the legal framework, financing, civil and mechanical engineering, commercial developments and the plethora of studies which have been made since the Second World War. I say this because the railway industry is unbelievably complex - the internal interactions between various parts of the 'system' are closely interlinked and the interactions between the railway and its customers (both passenger and freight), its neighbours, the general public, its suppliers, the legal and regulatory framework and funders are myriad.
What isn't clear to me is the background to the Ph.D. topic. Are you approaching it from a financial perspective, from an economic perspective, from a sociological perspective, or political, organisational or technical perspectives? Your approach will obviously differ considerably depending on the study's emphasis.
I wish you every success. And start writing the thesis NOW, it can always be changed as it develops. Don't do all the research and THEN start writing - if you do you will never finish...!