While I was writing my How to Write a Gamebook series, I emailed Ulysses as he has written the longest gamebook I can find - The Diamond Key clocking in at a whopping 1000 paragraphs. He has also written an amusing serial of scifi adventures which begin with the Wrong Way Go Back. Here is what he has to say about his writing process.
The Diamond Key (tDK) was my first gamebook and it's large size is mostly the result of inexperience and inability to plan. I started with an idea of a journey with several componants, and vague ideas about what I wanted to happen in each componant. My writing style is very organic, I usually just start and see where things go as I use intuition and spontaneous creativity. With tDK each leg of the journey is in effect a mini-adventure since they all have the same start and end points. In that respect the size of the book is not so impressive.
In retrospect, tDK would have benefitted greatly from the kind of probability planning you seem to be talking about. There are several paths which I realised later are so difficult to get to that it is possible no one has ever played through them. Since the Diamond Key offers so many paths to success with the best ending available without the need to find the obscuure paths, those obscure paths don't really add to the book since they are rarely if ever experienced.
If I was writing a similar gamebook now I would make it more structured in terms of how different paths contribute to different endings.
In terms of planning out the gamebook, I start out with a vague idea about how it works. For example in something like Wrong Way Go Back, My initial idea was that you were on a space ship and had a limited amoutn of time to escape. Various actions would waste time without contributiong to escape. Then I started writing. As I write I basically put myself in the shoes of the character and come up with some options. After I have decided on the options, then I decide if they are helpful or not and write accordingly. In this way the story progresses and for Wrong Way Go Back (WWGB) was all done in this way.
For longer stories there tends to be a little more structure overall based on different locations. For example in the Golden Crate I knew there were three basic locations: On the ship, on the planet where the escape pods crash, and finally on Amorphonon 12 for the finale. Each location is written about in turn in the same way as WWGB, and can have several exit points, giving several entry points into the next location. As the paths expand, I normally write them simultaneously, e.g. write one option on one path, then another option on the other (generally following chronological progress). This then allows me to decide when/how to link back into one or two main paths.
My method for managing all of this is to use pen and paper to create tree diagrams with branches for each of the choices or consequences. I assume everyone does becuase I can't imagine any other way of doing it. I label the nodes with codewords or items were applicable, so I can see for which paths downstream the codeword/item is valid. Once it's all done, I check it by reading through and recreating the tree diagram. There are always mistakes.