Congrats on getting the new machine. I'm not sure if there's a question in your post, but I can tell you that After Effects and Invigorator are NOT yet written in universal binary code, so they'll run under the emulation portion of the operating system. It's called Rosetta.
AE's performance under Rosetta will likely be significantly slower than it will be when Adobe and the plug-in developers make the transition.
I'm looking forward to that day, but I believe we'll have to wait until the first quarter of 2007 to see After Effects or the CS3 bundle.