Best way to control graphics synchronized to video cue points

Hello,
I've recently completed (well, 'completed' is a strong word)
a phase one implementation of a synchronized video presentation
using After Effects and Flash. The basic idea driving the
synchronization of cue points to motion graphics revolves around
creating a listener in the following fashion:
var listenerObject:Object = new Object();
listenerObject.cuePoint = function(eventObject:Object):Void {
// Put any code you like here
trace("Cue point name: " +
eventObject.info.name);
my_FLVPlybk.addEventListener("cuePoint",
listenerObject);
and then using the cue point name to play a variety of
movieclips at the appropriate time in the presentation.
The video presentation had four sections, each of which could
be arbitratrily browsed to at any point in the presentation, so it
was important that the the movieclips did not need to play in order
and that they could be interrupted at any point without an visual
confusion.
I dealt with this two ways (I am sure these are not the best
ways, which is why I am writing this post):
First, every single movieclip was already on the stage from
the outset, stopped on the first frame, with the alpha property set
to 0 (based on Aran Balkan
http://aralbalkan.com/444).
The final frame of each clip had a gotoAndStop(1) action on it so
that when a clip finished playing it 'reset' itself. I also wrote a
"rewind" function which pretty much did the same
thing whenever a user clicked on one of the navigational tabs.
For a first iteration, this worked pretty well, and it
impressed enough people in my organization (university) that now
the President wants to deliver a similar message. It seemed prudent
at this point to ask a general question about best practices in
this area. I am working with the full Master Collection suite, and
can target later versions of the Flash Player (I believe I can use
AS 3.0, although I will have to learn it). One thing that I am
hoping any pointers you guys might have will cover is this:
How do you handle starting/stopping/pausing of the video and
also make sure any currently playing graphical assets also
start/stop/pause on cue? I was thinking of setting a variable on
the second frame of each movieclip, something along the lines of
'nowPlaying = this;' and then resetting that to null at the end of
the clip and in the rewind function, then using that variable to
control the currently playing clip (would have to bu just one, I
imagine).
But there has got to be a better way. I have some down time
to do research and to experiment, but it is going to be very high
profile when it rolls around, so I thought I'd send out some
feelers.
Has anyone done anything like this? Seen a better way? Etc .
Thanks so much.

Best practice is to keep one single file as long as humanly possible.
In this case, you "branched" a version for another format; I'd suggest you don't edit that any further (apart from the formatting stuff you mentioned), but inform your client this version is to be worked on. Work on your "real" version until it's really really done, and only then make other versions.
It's a different story (no pun intended) if the transition between the two versions can be automated; that way you'd still only work on the 'real' version, but then you could generate the other with every edit you make -- you should still not be doing any work in the dumbed-down version.

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