Multiple sites knocked down to PR0 and how to get them back

Over the course of the last 6-8 months several blogs and websites of mine have been heavily penalised in terms of PR, this was both before and after Google Penguin.

These blogs had a wide range of PR, most were around 1-3 and a few were even 5 then around early December there was some large update that knocked several of the PR5s down to 3 and the lower ones down to 1 or 0, then again after the Penguin update many more were reduced to 0. Im pretty sure why this happened as there were several things that were going on these sites that broke Google rules such as unrelated links and they all passed PR (ie not using nofollow tag). Also I had a site that I think Google saw as being similar to BMR as this site had its Google indexed pages and traffic drop significantly around the same time the story of BMR broke. Also I had 2 big sites that were PR5 until they were dropped to 3 in early Dec with banners on that penalised site and around that time they went down to PR0.

For the last month or so I have been trying to fix these sites up and get their PR back.

I have removed as many links as possible and/or nofollowed the rest.

I have removed all connection with my site that was similar to BMR to my other sites eg all links, banners etc connecting them gone.

What else should I be doing? Is it just a matter of waiting?

How about links within content? Do they all need to be removed too?

Also, I need to point out that very few of these sites saw their traffic decrease, it was just their PR, I never received any warnings from Google either.

Any help or advice would be appreciated.