I don’t know if you have done this already, but Google maps for Tokyo is absolutely amazing when it comes to which trains to take. Yes, it can be a bit troubling to change trains but if you follow signs at the station itself its not that much of a problem. There is always someone either on the platform or at the ticket window to help as well. Everyone is really friendly.
I would also suggest that if you can avoid Shinjuku station that you do so since it can be quite confusing.
Also make sure that you have some sort of mobile internet while you are here. It makes a world of difference.