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Hi I'm not so sure it's Penguin because as a whole the site hasn't been hit, in fact organic traffic to the site has grown. The problem stems around a small hub of parcel related pages. The drop first happened when we changed these to affiliate pages; we then removed the affiliate links as detailed in my original question and tried various other ploys all to no avail. When you say we have a load of exact match keyword phrases in our on site anchor text you're not implying that this is somehow a bad thing?? Surely Google can't penalise for giving good on-site navigation??

I would choose the .com and create the /us/ subcarpet (targeting the US via GWT), in order to give to it an initial boost thanks to the authority the .com site already have. I would be sure to pay attention to all the classic issues of International SEO, especially I'd try to avoid duplicated content, and surely will implement the rel="alternate" hreflang="x" in order to avoid as much as I can to see ranking the UK version of the site in the US.

Yes, one of my exact match domains outranks a much stronger domain even with thin content and zero marketing efforts.  It don't think it should and I don't think it always will outrank stronger domains.

Thanks EGOL...much appreciated.

Hi On the old design we had the same footer links - parcel delivery was a sub folder and remains as such. The only difference with the parcel hub is that when we rolled out the redesign we added affiliate links to the parcel pages only. Rankings plummeted, we removed them yet they've continued to fall! As all other rankings remained stable I can only assume it's some kind of affiliate penalty which seems a little crazy as we hardly went overboard (we had 3 on the page) and besides they were removed when we noticed the drop, so for the last 6+ weeks we've had no links on them yet the rankings are still woefully low...now approximately 550 compared to top 30 prior to the changes!! Very baffling!

Thanks Keri, I have heard that when engaging in such nefarious practices webmaster tools should be avaoided like the plague!

don't use meta refresh. Use a 301 redirect. Google 301 and htaccess. If you're using a CMS, there are plugins for that.