Should I link our .ie site and .co.uk site?

Selected answers from the Dumb SEO Questions Facebook & G+ community.

• 
  Ian Wortley: What would you do?
  
  I've got a .ie site and a .co.uk site. The .co.uk site is shiny new and is an exact duplicate of the .ie site. The only differences will be in physical addresses for the business, but for now they are exact duplicates.
  
  At the moment the .ie site is showing up in searches on google.co.uk rather than the .co.uk site.
  
  I was going to use:-
  <link rel="alternate" hreflang="en-ie" href="www.site dot ie" />
  <link rel="alternate" hreflang="en-gb" href="www.site dot co.uk" />
  on both sites to help clear up the intended audiences.
  
  BUT.......
  The .ie site has been penalised by Penguin (a year ago and they're just getting around to fixing it now). So I'm not really sure I want to link the sites in any way further than they are with the duplicate content.
  
  So, back to my initial question....
  
  What would you do?
• 
  Shawn Cohen: Maybe I've misunderstood Penguin, but wasn't that a penalty the devalued linking sites and indirectly affected sites being linked to? So in that regard, the .ie site was affected by Penguin but the linking sites were the ones actually penalized.
  If that's the case, it doesn't seem problematic to link from a site affected by Penguin.
  I really could be wrong here, just thinking through the nature of the penalties (Penguin v. Panda v. a manual spam action).
  As a test, do you think you could place the hreflang tags on a few pages and see how the .co.uk pages fare in the SERPs?
• 
  Ian Wortley: The penguin triggers were keyword stuffed backlinks combined with article spinning in this case. I don't think penguin was a case of devaluing linking sites alone. If that were the case, then a legitimate site could be penalised for having some links that contributed to a sites spammy overall backlink profile. It would mean that I could create a site and specifically try to get penalised by penguin, then build further links on competitor sites in an attempt to bring them down a bit.
  
  Also, in this case the site is not all that badly hit in terms of ranking overall (although they lost over 50% of organic traffic overnight), but is particularly hit for targeted keywords contained in inbound links - which happen to be the important keywords of course. So, even if the link is from a trusted source, the overall profile of the link text is rotten, which again makes me pause before believing that Penguin just devalued bad linking sites. Yes article farms got hit badly with penguin, but penguin did a lot more than just target the sources of bad links.
  
  I like the idea of testing a few pages, but I think that would still be enough of a signal that both sites were linked for Google to pick up on.
  
  I think I'll just have to go for it and get the penalty lifted as fast as I can so that I don't have to worry about it any more.
  
  Thanks +Shawn Cohen ; you've certainly made me think about it more. I should probably think then write, but that's just not me. I'm a stream of consciousness kind of guy.
• 
  Shawn Cohen: Haha, I'm glad what I wrote was of some value. I don't have enough experience w/ Penguin to contradict what you wrote so there's a good chance my understanding is too shallow for the situation.
  At any rate, good luck!