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Any advice/help appreciated!
Thanks in advance
If the sites are kept separate just for cross-linking purposes, it might look like you're trying to artificially increase your backlinks -- and that would hurt rather than help.
The new site hasn't got the same theme, though broadly both the sites belong to similar category, they differ thematically. And one more thing I forgot to mention is that the acquired site has got very good PR, will it be good in this case to use 301.
If both sites have got different themes, how will cross linking affect adversly
Is there a reason you want to keep the domains separate?
I bought a competitor's domain after they went out of business (but still have hundreds of backlinks and several very nice directory listings) and I 301'd the domain to my site.
The content was never identical, but we were competing in the same market with a vaguely similar theme. So by 301ing the traffic to my site, I've absorbed all of those backlinks, and all the backlink credit and traffic is applied to a single site, rather than divided between two.
I think it makes sense to have a single stronger site, rather than two weaker sites competing for attention -- even if they are cross-linking between each other.