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You can disallow the https portion in robots.txt, but remember robots.txt isn't always a sure fire way of not getting an area of your site crawled. If you have other important content to crawl from the secured page, be careful you are not blocking robots from there.

If this is linked to other places on the web, and the link doesn't include no-follow, search engines may still crawl the page.  Can you change the link in your navigation to no-follow as well? I would also add a meta noindex tag to the page itself, and a canonical tag to the https version.

No, traffic itself has nothing to do with rankings.  I am sure there is probably a correlation between traffic and rankings because more traffic = more exposure which can lead to more links - or to more user generated content on the site, if it has any.

I see you have noodp in the title tags, and as you said it has been there awhile, so I would assume that would have been updated by now.  It could just be taking a particularly long time to update.

Another guess is that it may be due to the main site's title at rickcase.com.  The title is 145 characters long:

Rick Case Automotive Group | Leading auto dealers for Acura, Audi, Honda, Hyundai, Mazda and Mitsubishi models at Ohio, Georgia and South Florida

It also includes the word Honda.  Occasionally Google will rewrite titles based on what they feel is more relevant.

Here is a post on SEOMoz about Google changing long title tags:

http://www.seomoz.org/blog/long-title-tags

Here is also a short post on Webmaster world:

http://www.seroundtable.com/archives/023139.html

I am not positive I understand the question - so let me repeat what I think you are asking:

You want to remove links from your homepage that link to inner pages of your site, and move these to another page on your site - I am assuming the intent is to create a kind of "resource" list of links? Because you are just moving the links themselves and not moving them around in the site hierarchy - the URL is staying the same.  Right?

If I am understanding correctly, then the answer is...it depends

Do the pages that you are moving have a lot of authority because there are a good amount of backlinks to those specific pages, or do they have a lot of authority because of their proximity to the homepage (1 click away).

I suggest running each page you are considering moving through Open Site Explorer and checking the incoming links and # of linking domains.

If it is the latter, then these should continue to rank well, but over time may begin to degrade in authority as they are now more clicks away from the homepage, and the PR of those will now spread to deeper pages of the site.

If it is the first, then there shouldn't be much of an issue, though you still may see a slight degradation over time because they are not as close to the homepage.

Overall, you shouldn't see too much of a loss.  You can try to mitigate any losses by building quality links to these pages directly.

As Gamer07 said, Google is pretty good at detecting these, so many the affiliate links themselves should not give much SEO benefit.  However incorrect implementation could lead to issues with duplicate content.

If you are going to send your affiliate links through a different directory than the main page - such as /affiliate/ then you should make sure that you block this directory with robots.txt - as an extra precaution I would add canonical URLs to the page since you cannot guarantee all incoming links will be no-followed.

Personally, I think the best method would be to use the one main page that you direct both visitors and affiliates to and then add a hashtag (#) to the URL for affiliates and include their affiliate ID after that.

• Edited portion of last paragraph (left out a word) and corrected spelling error

Okay, I took a look at the plugin Ben recommended, and took another look at the SH404SEF one.  The free one Ben recommended (http://extensions.joomla.org/extensions/site-management/sef/1063) looks like it can help out with some duplicate content - but what I recommend doing is getting the SH404SEF here http://anything-digital.com/sh404sef/features.html because it allows for setting up canonical tags and also gives you the option to add the rel=next feature to your paginated pages, which is one of your problem areas.

One thing I noticed though is that it specifically states it "automatically adds canonical tags to non-html pages" - so that means it will apply it automatically to Joomla's defaul pdf view, etc.  While this is helpful, it may not solve the full issue of your duplicate pages with the undefined and "/%5C%22/" issue.

It does however state that it "removes duplicate URLs" - how it identifies and removes these, I am not sure.  You may want to try it out because it is useful for other optimization tasks - or contact the owner for more information.

If the tool doesn't recognize and remove the duplicate pages caused by /undefined/ and "/%5C%22/" then you should disallow crawling of these in your robots.txt file.  While you are in your robots.txt file you should remove the /images/ because you want those to be crawled - Joomla adds that in by default.

Because a lot of these pages have already been crawled, you should do a 301 on the duplicate pages to their matching page.  This sounds like it will be a long process - this may be aided by the sh404sef plugin - not sure.

I just want to also add that I am in no way affiliated with any of these plugins.

Joomla has soo many dup content issues, you have to know Joomla really well to avoid most of them.  The biggest issue is you didn't enable the SEF URLs from the start and left the default index.php?option=com on most of them, which stuffs your URLs full of ugly parameters.

You can still enable this in your global options and with a quick edit to htaccess  - but it will change all of your current URLs and you will need to 301 all of them, so that isn't a great option unless you are really suffering - and depending on if you are using J 1.6 or under, this is a time consuming nasty process.  Also this is unlikely to get rid of any existing duplicate pages - but may make dealing with them and finding them easier.

I don't see the specific examples you posted though, where are you seeing "undefined" and "%5C%22/ " ?

You should implement rel=canonical on the correct version of each page.  I recommend SH404SEF which is a Joomla plugin and makes this process easier - but it isn't free.  I don't know of a good free plugin that does this, and Joomla's templates make doing this manually difficult.

Looking at it quickly, I also didn't notice any articles that were paginated, but you should try to follow the rel="next" and rel="prev" for paginated pages.  This is likely something you will have to edit your Joomla core files to do.