I think the only good way you are going to make any headway with this question is with an Official Railroad Guide. That was a huge book which listed all the railroads in the country.It might have been monthly, it was at least quarterly.
It is probably still published, perhaps even with Amtrak info. I do know it did that at least the first few years of Amtrak. But I know you are thinking about a period long before that.
You can perhaps find them at railroad shows, perhaps on e-bay. But these are the magic words: Offical Railway Guide. Be alert to that, try to find a good price for one (I am sure they will be expensive) and that should help immensely.
You will find, even with all that info in front of you, that the question you are asking will not be easy. In fact you will probably get so involved in the details of each railroad and train you will forget the original question!!