If you are on CS5 you can open the red file directly into After Effects and key from there, no conveeting needed. Or if that is too heavy a TIF sequence exported from Redcine could be good alternative.
I'll try a tiff sequence.
As the R3D file is black and white, and I'm not sure how to convert it back to colour. Originally I was aiming to take the R3D file directly into AECS5, until it showed up as black and white in AECS5.