I’m using Twine myself (http://www.gimcrackd.com/etc/src/), so I can see how everything branches, and there is zero programming involved (though you can use a basic command such as <<choice “He goes right.”>> to give choices and cut others off). Then I’ll add the story to MS Word, and convert it into a Kindle file. What RVallant mentioned to me a few days ago, GBAT (http://www.crumblyheadgames.co.uk/the-gamebook-authoring-tool/), is also an option.
Of course, there’s also Choice of Games’ very own Choicescript you can try as well.
What others have said too is good advice. Try not to be over-ambitious, though it’s fine if you don’t mind the work and think you can handle it. Thinking you can handle it and being able to are two different things though.
For instance, I’m writing a heavily personalised interactive story at the minute (working on two, one of them less interactive and personalised). In the 1st chapter, I’ve done 356 words, and there’s the potential for around 8-9 different branches already as I’m trying to give the reader options to develop their character, I’m guessing (I’m only writing one path through currently, hence the guesswork). When a choice is made, unique text needs to follow it (I’m not saying it does for you, but because of the way I’m handling things, so choices matter, it does for me). So it is easy to imagine how things can spiral out of control. That’s why it’s probably best to rein in your ambitions because if I’ve already got that many branches from a few hundred words, imagine how many there would be over the course of a longer work? The positive side is I don’t need to worry about coding, but yeah, I imagine people would love to see the chart detailing the branches if it ever gets finished.