Yes it helped! Thank you very much I really appreciate the time and effort you put into responding. I just have a few additional questions.
1. I expected some sort of penalty because a sample of the backlinks I analyzed (which their previous SEO firm built) were of the spammy blog comment variety or 404's (I reckon it's best to just disavow these ones?). Is there a template or something I can use as a guide for emailing webmasters a backlink removal request (With the proper instructions of how to within it). Also thank you for recommending Link Detox. What do you thin k of http://www.removeem.com/self-serve.php as Thomas suggested? It seems to be vetted by Moz and they have an automatic service for contacting webmasters. It must be insane trying to contact 4000+ webmasters. How do you even organize something like that?
2. I'm afraid I was not being clear. My issue is not domain migration after all. I think the issue is just a canonical issue. Basically they were using a very bulky CMS and I used wordpress to redesign their website. I also moved them to a faster dedicated server. The nameserver has not yet been pointed to the new server yet. The problem is some of their old URLs look something like oldpage/old-section1.html and on the new wordpress site everything is neater /more-descriptive-new-page/ So this is just a canonical issue correct? I just have to sort through all their pages and find the corresponding one on the new site?
3. I put up a temporary redirect just to do some quick A/B URL split testing on the entire website. I thought it might be a bad idea but I wanted to get some preliminary results in as visual website optimizer did not do the job for me that I wanted.
