I feel your pain. I loved Director and used it for all sorts of projects, including multiplayer games and 3-D. McDonald's used it for menus and it was also used in ST TNG for animated screen readouts, plus it was used for a number of highly interactive movie promo sites, such as the site for the original Mission Impossible.
It really has outlived its usefulness and the output tended to be bulky. Back in the days of CD games when everything was on the disc, it was great but it was dead slow on the web. It looks like your type of project is pretty much Director's last gasp.
For your purposes, the best thing I would suggest would be to use After Effects to output as video with markers and create a shell app that would control the playback between the markers. I'd recommend Hype for this, but Hype doesn't (yet) output markers. The unattractive alternative would be to use Hype to output to MOV, create a text doc for the markers and paste this into the video using QT Pro.