In the last couple of years I have planned the route for several long distance hikes all over Europe including a "thruhike" of the UK from John O'Groats to Land's End of 2,000 km and a 4,500 km hike across Western Europe.
I had ample opportunity to learn how to plan your own route, what (online) resources to use and what logistical problems to solve. I want to share my experience with other prospective hikers planning similar long distance hikes and have written a comprehensive article about route planning on my blog. As this article contains a lot of web links and those are very awkward to embed into BPL forum posts I just want to refer you to my blog. You will find the article here:
How to plan your own route for a long-distance hike
The article is mostly geared towards hiking in Europe and contains links to various European internet resources but the description of the planning process might be useful for all hikers planning their own routes.
I am always looking forward to feedback and of course will answer further questions.
Hope this will be useful for other hikers!