Planet13 - 10:53 pm on Sep 19, 2013 (gmt 0)
You can submit a disavow file yourself to google. No need to drop five large to do it.
Before you start developing any new shopping cart (or splitting it off into two or what not), you really need to get things figured out.
- There are several free tools out there to help you find your backlinks.
- There are several free resources out there on what a BAD backlink is (in google's eyes).
- As pointed out above, you could have a Penguin demotion / affliction without a notification in your webmaster tools of a manual penalty.
The best thing I can recommend is look closely at your google analytics for google ORGANIC traffic and see if you saw significant drops (25% or more) in traffic from google on:
April 24, 2012
May 9th, 2013
May 22nd, 2013
(Note: May 9th is not an OFFICIAL Penguin update, but it seems that many people who were hit by Penguin 2 on May 22nd, 2013 were also hit by the May 9th update).
Also, you need to get as much previous work from your SEO company documented. If they built links - maybe they did, maybe they didn't - you should get as much info as you can about what, where, and when they did it.
In my opinion, until you get this straightened out, you should avoid putting any more serious resources into your site. You need to figure out what is wrong FIRST before you can fix it.
Just my opinion.