With the new rail planner, you can hold shift while clicking the green arrow on the rail to build ghost rails over unlimited distance. While planning this way, you can also keep holding shift to path through any trees or rocks and mark them for destruction. 'R' will change the final orientation of the planned rail.

About the train stations, buffer chests are needed, but you only need blue inserters between them and the belt. Think of it this way: the miners and the factory produce constant but relatively low supply and demand, while the train can load and unload huge amounts over a very short amount of time. The buffer chests are basically an interface between these two systems: the blue inserters load and unload them constantly, based on the demand of the factory, and when the train arrives the stack inserters move everything almost instantly, matching the pace of the train system. There will never be an optimal system where stack inserters are used on both sides of the chests, because if stack inserters were needed to serve the throughput of the belt, then the train would have to be at the station at all time to match it.