I have been cleaning the seals on my CC, and noticed the one stuck to the rear window is starting to come up, so I am concerned the effectiveness of the seal is not as it should be. I have not been able to find a part number, nor a used one for sale. Checked Google and Ebay.

Anyone have any clue on this ? Is there a schemeatic for the roof with the part numbers for the seals ?

The alternative is to remove it, clean it, and re-stick it down to the glass.

The CC has its own section on catcar.

https://www.catcar.info/ford/?lang=en&l=

I'm not sure exactly which seal you're after.  If you select the car, then body & paint, then either glass or possibly roof opening.

With the CC being built in quite low numbers I'm not sure you'll find parts on the shelf even with the part numbers.  You'll probably have to ask your local parts desk specifically, but it does help them if you've already got the part numbers.

Thank you for the link to Cat Car, it led me to the right part. While it is not available anywhere online, at least I can go to a dealer to see what they suggest.

Also, I managed to find a picture, which shows it is taped to the screen, so that means I can with confidence remove it, clean and stick it back down with some new automotive tape. 

Be aware that many of the seals (and other parts) of the Focus MK2/MK2.5 CC are no longer available from Ford. 

Quite soon after the Focus MK2/MK2.5 CC went out of production many of the CC specific parts became no longer available when Ford ran out of stock. I have seen CC's with minor accident damage being scrapped because parts like the rear bumper and taillights were no longer available from Ford.