Phillip,
Brian Ford has helped me out quite a lot, so if he can make a solution to your problem it will do it. I had a somewhat similar issue crop up and thought you might take a similar approach. I needed to transition from a lower third headline to a bite font on a higher layer---my designer suggested using a separate Take ID with the transition effect only. A script I found here (probably from Brian Ford, by the way) made it work.
On my primary scene director, at frame 70, I inserted a pause. At frame 71, a script event with the following script:
Dim MySequencer as xpSequencer = nothing
MySequencer = Engine.Sequencer
Dim MyTakeItem as xpTakeItem = nothing
MySequencer.GetTakeItemByID(1235, MyTakeItem)
MyTakeItem.Execute()
Now in the Keyframe Editor, you would want a series of keyframes to zero the alpha values of the objects you want to clear after your pause is released. Timing of this might be tricky, but quite doable.
Back on the primary scene director, at frame 91, a TakeOffline event.
If you take your animation back to AfterEffects and reverse it, trim it down to just the effect and make a dissolve up to what is now the head, this should work as your transition Take ID.
If you loop the video on a secondary scene director, with a Jump to frame event, you should be close.
I failed at attaching images here to support my description, but I could email you that if it would help.
James.
#XPression