I like this idea! I’d say play around and see what ‘writes’ easiest – or look at other text-based games to see how they balance text/choices. (If you’re hesitant to spend money, you can still check out the demo for any CoG/HG – or look at some of the works in progress on this forum. Totem Force has a nice balance of story/choices imo that might give you some ideas, but there are a lot of different approaches I’ve seen.)
I played around with Twine a little once upon a time, and do miss the timer function! Remember that people have different reading speeds, though, and you will tend to speed through your game when you test because you’ve seen all your text already. (I replayed my old timed game recently and utterly lost – that time limit was way too tight) Maybe have a button to display the choices that also starts the timer – that way your players have plenty of time to read the rest of the scene before seeing the choices and making a decision. And can you display an active counter/timer on a page? I don’t remember…
EDIT: This recent thread about what ‘person’ to write in might interest you: