Can you match move or track a scene with AE and use that information in AE to work on the clean plate process? Will AE give you a 3D camera to work with in this case or do you need something like Mocha to do this? So if I had a character as a stand in for a shot and wanted to paint him out and add a 3D character in, I would need to track the shot, and then take that 3D camera information to create a clean plate to put the CGI character in, right?
AE tracking and Mocha tracking will give you 2d information. For a 3d camera match you need a 3d tracker - Camera Tracker from the Foundry works pretty well in AE. Boujou, SynthEyes and and a few others will do the job as well. SynthEyes has some cool features that enable you to create a clean plate.
As far as replacing a real person with a 3d character, C4D will allow you to import AE camera data.