I need an expert opinion from an SEO vetran or IT person who has actually done this with a large ecommerce website. I have a potential large ecommerce client who wants to basically duplicate one site's shopping cart, product listings and all because they have one domain which has more localized terminology in the domain and they want to have the same products on a more general one. Both domains have lots of unique backlinks and they are different. The top pages will have different titles, but the shopping cart and products will be the same. Will Google filter out the products in search on the second site since they have already indexed the products on the first? What are the consequences? Will their "trust rank outweigh" outweigh filters? I realize this might not be enough information, please ask any questions you need so you can have an informed opinion.
The domain where they want to duplicate is new ? If it is not new, what kind of backlinks are ? if they are related to something else then they are almost useless. The client is open minded ? My suggestion is to merge those e-commerce sites, and direct the link juice from one to another making 301 redirects. Working on both sites will need more money, more backlinks, etc.
The site which will have the dup shopping cart is not new, it has 60 backlinks. The site which the shopping cart will be copied from has 4000 backlinks.
I would advise them against it. I would 301 redirect the links from the site with 60 backlinks to the domain with 4000 backlinks and call it a day. You are going to be introducing duplicate content issues. And each time that you add a new page, you won't know which of the two sites will get flagged as original and which will get flagged as duplicate. There is no advantage from an SEO perspective of having 2 sites that with lots of duplicated pages. If they pages are duplicated Google will typically filter one of them out of the results. If they absolutely insist on keeping both domains then I would pick one to be the primary domain that you want to appear at Google and use the <link rel="canonical"> to set EVERY page on the site's canonical URL to the version on the primary domain. Google just announced the <link rel="canonical"> can now be used for cross-site canonicalization. Of course, this ONLY fixes your issues with Google... since neither Yahoo! nor Bing have implemented support for <link rel="canonical"> even though they said they would support it when it was first announced.