Feel free to use AE. Just chop up the audio in handy pieces so you don't end up with endless waiting when AE mixes it for preview. I'd still use a modular approach and keep segments in separate projects. Depending on what's required, you could easily end up with 500 comps and pre-comps for half an hour and that could be pretty confusing...
After Effects is for working on shots and on occasionally sequences. Short sequences. I just did a dynamic text and graphics animation that was 2 minutes long. It consisted of 4 separate AE projects, the longest was just under a minute and contained more than 900 layers. The other other sequences were different thoughts (scenes) in the script. Turned out that the project needed to be re-cut less than 7 days after it was completed. It took me just a few hours because I only had to dig through one of the sequences, change the audio, retime a few slayers, then jump to PPro to change the order of the sequences, and TO Audition to re-mix the audio. It was a lot easier than it would have been if the entire 2 minutes was one project. I WOULD highly recommend that you do not try and to the entire project in a single AE project.
Divide your script up into sequences, plan the shots, set up a flawless file structure and naming convention. Build your shots and sequences. Give them handles (extra frames at the head and tail so you can edit and fine tune the flow later). Render each shot, then put the footage in Premiere for editing. Do the sound track in Audition, and you'll be on your way to a professional approach. Dynamic link is OK for a shot or two in a sequence but completely unsuited to a long form project. Treat the project like you would treat a traditional film. AE becomes the camera, rendering becomes sending film to the lab, and editing stays editing.
Thanks for the insight. Really appreciated!