I have 2 sites the have ranked well on google since 2000, that is until this past update.
I think what they have gotten me is that the secondary site links to the primary site's shopping cart. My plan is to set up the secondary site on its own shopping cart and delete the links between them. My question....
Both of these site will be hosted on the same server but will have a different IP address. This along with deleting the interlinks and basically making them otherwise independent of one another.
Will google still be able to detect they are from the same company? Or will the dedicated shopping carts and different IP addresses be enough to fix (my assumed ) penalty.
Google did not drop either site, but my rankings dropped significantly and the only think I can attribute it to, is the interlinking with the shopping cart.
TIA

Wait until all the screaming dies down before you do anything. Your sites could come right back whenever Google finishes whatever they are doing.

Will google still be able to detect they are from the same company? Sure. google is a domain registrar and has access to all the domain registration info.

google never forgets little tid bits of info like, who was registered as domain owner to such and such domain in such and such year.

I think what they have gotten me is that the secondary site links to the primary site's shopping cart. I am going out on a limb here without having seen the site in question, but I think it is safe to say your on the wrong track here.

I don't believe that google is ever going to start discounting or penalizing links between sites that are only related by who owns them, as long as the linking structure falls within "normal" limits.

If I were you I would be analyzing my backlinks, to see if I was a casualty of the new "nofollow" tag or some change in EXTERNAL linking structure.

Don't let the google fear mongers scare you into doing something you'll regret later.

Here are the 2 sites in question
http://www.hubcaps-wheelcovers.com
is the primary site.....and
http://www.hubcaps.biz
Is the secondary site.
The second was created to attack common spelling variations of my product.
Yes, it is pretty much a duplicate site.
When you get to here on the second site is where the links exsist. (at the "order" buttons). There are several hundred of these links. I have been careful not to link any photos or any other linkable items to the main for fear of being red flagged.
http://www.hubcaps.biz/honda_civic_hub_caps.htm (is one example).
I didn't realize that robots spidered shopping carts until I started monitoring my logs and notices that slurp and googlebot were making frequent visits to them.

so remove one and 301 it to the other.
You can't expect google to say it's OK two dupe sites.

Here are the 2 sites in question
http://www.hubcaps-wheelcovers.com
is the primary site.....and
http://www.hubcaps.biz
Is the secondary site.
The second was created to attack common spelling variations of my product.
Yes, it is pretty much a duplicate site.
When you get to here on the second site is where the links exsist. (at the "order" buttons). There are several hundred of these links. I have been careful not to link any photos or any other linkable items to the main for fear of being red flagged.
http://www.hubcaps.biz/honda_civic_hub_caps.htm (is one example).
I didn't realize that robots spidered shopping carts until I started monitoring my logs and notices that slurp and googlebot were making frequent visits to them.

so remove one and 301 it to the other.
You can't expect google to say it's OK two dupe sites.
Umm OK. If you would have read earlier post you would see each site has a purpose... Attacking variations of spelling for the product. I'm not asking for easy solutions and am willing to create another shopping cart to make the other site more independant. I just want to see if it would be worth it before I put a weeks worth of work into it.
I would even be willing to give the site a total makeover but deleting is not an option. Yahoo and MSN don't seen to have a problem with them.
Basically the questions is..are the (shopping cart) links hurting the ranking (maybe the reason for the demotion in rank) and is it OK to host both sites on the same server with separate shopping carts and different IP's? Would that pass muster?

First let me say that the two sites are NOT duplicates.

Basically the questions is..are the (shopping cart) links hurting the ranking... Not that I can see. Looks like your running an “off the shelf” cart, with few (if any) script alterations, nothing that I believe would cause any ranking problems.

... is it OK to host both sites on the same server with separate shopping carts and different IP's? Would that pass muster? I know of a lot of different sites that do this same kind of thing without any problems.

I am assuming that your main targeted keywords are “hubcaps” and “hub caps”, I see your #2 in google for “hubcaps” but nowhere on the first three pages for “hub caps”.

Looks to me to be a problem of on-page semantic text and anchor text.

Also if it were me, I would do some work on your internal linking structure, your not utilizing all your resources.

Too be honest, I think using two different domains the way you are is just shooting yourself in foot.

Why not use just one domain and use either sub-domains or directories to do the same thing?

If you only use one domain you would not be splitting your linkpop between two different (but similar) sites and I have seen where that can become a problem over time. Your links are already leaning more toward the .com site, so in my opinion, your just wasting all the back links to the .biz site.

Thank you for your reply. Much to consider here.

Having two websites regardless of their content, on IPs form the same owner and having placed links to both websites on different external pages might have hurt your websites in the recent update, especially for the search term used in IBL.