you can render with an alpha channel, but I don't think it will speed up your render any. In the camera properties (under the container in the PWS), go to Output Options > Buffers and turn Alpha to ON. Make sure you render to an image format that supports alpha channels, like TGA.
Even for AO, a render time of 40 minutes for that model sounds really excessive. What resolution are you rendering to? How many passes? Usually, 5-9 passes will be plenty for this kind of animation.