I have a bunch of video files from my Canon 7D that I need to convert and then edit in After Effects on a PC.

Does anyone know the best settings to convert the H.264 files to? The ProRess 422 is my codec of choice for use within FCP, but this file type won't import into AE (the files have some error when they are trying to import).

Any suggestions would be greatly appreciated.

If you have the Prores PC (reading) decoder downloaded then prores quicktimes should work in After Effects. It's available from Apple here:

Apple ProRes QuickTime Decoder 1.0 for Windows (http://support.apple.com/downloads/Apple_ProRes_QuickTime_Decoder_1_0_for_Windows)

Other than Prores - your choice of codec really depends on the sort of work you need to do.