1. On the driver's side, follow the lead for the clutch line pass-through. There is a large enough hole there that you can actually see light through it, very easy to use. That should work.
2. You might try under the rear seats, if I recall there's a pretty large space there when you flip up the seat. Other than that, you might be stuck.
3. I don't think this is recommended. Check out the FAQ's on this site for more info about trying to hook up aftermarket components to your factory system:
http://carstereohelp.net/gotquestions.htm
If I were you, I would just wait until you have your new HU. It *might* work the way you're thinking, but I've found factory bose systems to be pretty finicky.