The skylands central rail station seems to be 100% functional now. Please report if there are any issues.
The tracks however are flawed still. I am not sure what it is but there are no stations on the copy-pasted tracks and some holes. I will have to try again but I might be running into the limits of the system by trying to paste a 3200 x 5 x 3 large block into unloaded chunks and hoping that it works as expected.