The problem with Interactive Hyper Narrative

What's the problem with Hyper Narrative in an interactive space?  I'll tell you what he problem is.  It's a great big pain in the ass. That's what the problem is.  I also chose to explore this for my Thesis in Emergent Media. This is what I've been spending the last number of months working on.  I knew it was going to be difficult and I think I'm raising more questions than answering them. Here's a little background for the uninitiated.

I'm currently building a short story that's meant to be read multiple times.  You can read all the way to the end of the story, making choices along the way and come to a (hopefully) satisfying conclusion. If you re-read the story and make different choices you will come away with a more complete picture of the events that transpired.  Nothing earth shattering here.

Where I'm trying to push things is through the notion that the choices you make as you are reading will unknowingly shift the story from one track to another, and that the protagonist appears to be the same person in the same world experiencing a different reality of events.  Where on one track the protagonist is a high-functioning success, another version is struggling. To further complicate matters, it's possible to meet your other selves and through that discover that you all have the same agenda. Ok, it's a little weird, but I'm hoping it at least comes together as an interesting experiment.

I'm a little over half-way done and what I've learned so far should have been obvious to me.  Academically, I knew this was going to be difficult.  Writing one decent story is hard enough.  Writing three at once is clearly more complicated.  Weaving them together so the reader can jump around and still follow what's going on leads to vomit inducing headaches.

To that end, I've come up with a few rules for myself to keep the project on track and in scope:

1. No Dead Ends - The story continues to move forward.  There are no choices that lead to a premature and unsatisfactory ending to the story.
2. As an extension to rule #1, time must continue to move forward. This is a departure from more traditional forms of Interactive Fiction where the player could move back and forth between areas as much as he or she wants.  In this format the story would only progress when the player did the right combination of actions (like finding the key that unlocks a door). This has led to some trouble making sure the choices presented are interesting.
3. If the reader jumps to a different track, the story can and should reference what the reader (and the protagonist) knows from the other track. This is extremely hard to do and difficult to keep track of, but I think it has added a lot of flavor to the story.  In Inklewriter, the tool I'm using to build this, tracking variables is fairly simple and highlights a major difference between Hyper Narrative and something you would experience in a Choose Your Own Adventure book.
4. Keep It Short - The interactive nature suggests that choices need to come quickly and regularly.  Too much time reading the prose tends to encourage the reader to skip ahead to the choice.

I don't yet know how all of this is going to pan out.  And now that I'm in the thick of it, it has become very hard to show my progress as anyone reading through it will see less than 1/3 of what I've actually produced and won't have a full picture.  I can only hope that once it's done it will make sense.  I think it will.