Sorry! I am rather new to Internet Archive and still finding my way about myself although it seems to have a lot of useful books. Try this link http://www.archive.org/search.php?query=Privy%20Council%20Scotland It's possible the volume you need hasn't been added but this should take you to at least some of the volumes!
Ezziej, the Registers of the Privy Council Scotland have been published with name indexes and are available in some reference libraries here in the UK. I just discovered you can also download the volumes as ebooks from http://www.tannerritchie.com/books/rpc.php (for a fee) and they also appear to be included on the Internet Archive at www.archive.org for free.
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You might be interested in the England group - it's at http://www.genealogywise.com/group/england
There are links to the county groups on it too.
There is a small section on Covenanters in the NAS guide to Crime and Criminals at http://www.nas.gov.uk/guides/crime.asp#covenanters which might lead you to further useful records. You could also search the NAS catalogue at http://www.nas.gov.uk/onlineCatalogue/ for more details of what is available.