It's taken 2 days for my dear old Mac to render 400 frames but it has done it and it looks good. Rendered a ProRes 444 HQ .mov file as well as a separate alpha ov outvof C4D. Brought into Shake and plugged in the alpha. Found that I needed to use one of colour channels in the title node to get the alpha to work - this way though I was able to use a brightness node on the alpha channel to effect the opacity. Works a treat.
Rendered out the title minus the moon. Will have to adjust the timeline in FCP 7 to get the extended version in!
Next time around I am going to export a png image sequence from Cinema 4D as that carries transparency details - apparently image sequences are better.