You can find the list of the posts about a train seat reservation and a timetable resource. Please click the name of the post to get the detailed information.
You may find the links of the timetables by many train companies.
If you cannot find the timetable in List of timetable pages by the train companies, Hyperdia helps you. Hyperdia is a train and a flight route search engine. It is a bit tricky to use this but you can find all functions of this site by this post.
Reservation and fare calculation
You can find lots of resources about purchasing and booking a ticket at the window and online.
When you purchase a train ticket in Japan, a ticket is issued sometimes in Japanese. But it is no problem to read this post. You can find all information even if you do not understand Japanese at all.
This page explains you a basic rule of JR regular ticket. If you do not intend to use any train passes, this page is recommended before you purchase a ticket.
Many trains have reserved seat car and non reserved seat car. This post shows you the difference of these.
Many tickets are not available online. But if you use Cyber station, you can find an availability of most JR trains. It is a Japanese site. But you can find how to use this site by this post.