I have worked for NR in the past and still work with themdaily on civil engineering projects and do this sort of thing regulary. Best thing to do is to contact Network Rail outside parties; if you google “Network Rail outside parties map” it should link you to the right section of their website. The map contains all the regional contacts. I’m on hols at the moment and only have my phone but can give you more info later if you want.
I would expect you will need a basic asset protection agreement (BAPA) that will have an associated cost; the cost is a risk based review of your works/project and the risk to the railway. There is no upper limit, generally the closer to the railway and the higher risk of things falling on the railway the higher the cost.
To start you will be asked to submit a development questionnaire or similar, this tells NR about your work so they can estimate the BAPA cost, always put as much info on as possible otherwise they just assume and the cost goes up
Once you have a BAPA, and by the sounds of your works you would need to submit two further forms for approval;
A combined Form 002/003, which will cover the design, check and technical approval by NR for the scaffolding. These forms are available on the net.
And, a method statement/work package plan which will govern how the works will be managed Safely.
As I say I’m away at the moment but can help more if needed when I’m back. Hope the above makes some sense, difficult to write on a small phone screen