I'm with Killa on this one. You've already noticed problems and identified them. An overhaul can be tedious but if it needs to be done, it needs to be done. There's no sense in struggling on with a story when you know you'll be unhappy with the final results.
Just, I'd recommend making sure you know where you want the story to go and make at least a basic outline and a plan for getting there, or you might do all that work just to get bogged down all over again. 'The story really didn't get anywhere' is kind of a serious issue in any situation, but doubly so when we're talking about a CYOA.
I'm expecting (hoping!) to have this weekend entirely off so drop me a PM if you want, maybe I can look over some of what you've got if more specific suggestions are what you're needing.