From search engine journal:

"For blogs, I prefer a subfolder (http://www.seomoz.org/blog/) because the link juice which is sent to that blog is going to be naturally distributed to that main domain, and other subfolders under the domain.

Futhermore, the forum/blog will default logo, home page and other links back to the subfolder. If you set this up with a subdomain, by default, the links in the forum/blog itself will all point back to the subdomain. So, with a subfolder, both the inbound and internal linking structure favor the entire site.

With a subdomain, the forum or blog will be listed as a separate entity in the Google search results, which is good for owning the results and one’s reputation management. However, Google and other engines will generally not list more than two of these subdomains in the search results, unless those subdomains can prove to Google that they are independent and relevant entities."

If you don't know htaccess, redirecting the site to and from the subdomain can be a nightmare. If not setup correctly, your subdomain can cause you all types of duplication and strange URL complications.

Hope this helps!

While some of the moz tools are inaccurate, most are a pretty good starting point for discovering errors. We have run into the same issue, where server settings were not allowing the rogerbot to access the page or pages.

I always preach to use your heading tags like you would when writing an article in Microsoft Word, and use 1 H1 tag per page.

Main Subject Line that Includes Keyword or Mission

Words that explain the information you are trying to cover, and your "mission statement". Include higher amounts of keywords within first paragraph while not stuffing. Should also contain some sort of conversion statement or button

Secondary Information or Second Viewpoint

Words that include keywords and viewpoint.

Last Heading Includes Summary or Closing Arguments

Include high points of what has been covered

CMS sites often render out header tags like mad, causing you to have multiple H1 tags on a page. To check to see if yours is doing this, use SEO Browser. IMO, you can have more than one H2, as you may have multiple high level topics to cover on one page. Keep in mind, you can always use CSS to make

text render as a heading tag, so your page doesn't look goofy. For example:

If your h1 css looks like:
.h1 {
font-size: 28px;
line-height: 29px;
font-weight: bold;
}

then set up a div class:

.largeptext {
font-size: 28px;
line-height: 29px;
font-weight: bold;
}

and they will look the same, but not render an additional h1 tag per page. Use this for your sidebar and page styling areas that also render h tags.

I love these types of questions

It always gives me a chance to support one of my favorite tools, SEO-browser. This tool allows you to see what a search sees when they come to your site. What you see is not always accurate. Here is a quick crawl of your page in question:

http://seo-browser.com/index.php?address=http%3A%2F%2Fwww.seniorplanning.org%2Fassisted-living-phoenix-arizona%2F&button0.x=54&button0.y=9&button0=Simple

You can see that your H1 shows up high in the content, and that the image slider is not pushing your site further down other than visually. I don't think that the "above the fold" is as important as other areas of the algo. I have seen hundreds of sites do amazingly well with very large or fullscreen image sliders, and H1's after the scroll. As long as you are covering your main keywords in your content, H tags, meta and page titles effectively, I think you will be fine.

If you are going to do some edits on your site, bookmark that tool. It helps to see when sidebar headers or template headers are rendering out as h1, h2, or h3's.

This is actually really easy to test. Set up a basic version of each, and run the URL in this tool. Seo-Browser will allow you to see how your website is seen by a search engine bot. I have used this for TONS of sites, and never had it fail me when needing to see if something had to be changed. Once you copy and paste your URL in place, click the "simple" button. You can also sign up (it's free) to get more in-depth results.

As long as you have live (meaning read-able and not image based) text that is crawlable in your slideshow, you should be fine. Try it, and test using the method above. Best of luck!

If all the pages are not indexed, then yes I would assume a penalty. One of the more common reseaons a site gets penalized is due to improper linking, either inbound or outbound in nature.

If you do not yet have access to webmaster tools, there are still steps you can take. This is something you are going to have to do anyway, once you figure out what the penalty was for.

First place to start: links.
There are a wide variety of backlink tools out there. Here are a few you can try:
http://raventools.com/marketing-tools/link-manager/
http://moz.com/researchtools/ose
https://ahrefs.com/

Start looking for the spammy or paid links. How can you tell? Simple. If a link has a domain like rankmehighingoogle.com or something like that, chances are it's a bad or paid backlink. The example given is a silly domain name, but you will see some like that come up. If you are unsure of a links quality, manually visit the sites to see what they are all about. If the home page has a 0 or a ? for pagerank, chances are the linking site got hit with a penalty and you should disavow that linking domain.

Another way to test is to search for the linking domain in Google. If you search for a web directory site or linking domain specifially by their name and they are nowhere to be found, Google most likely hammered them for some practice they were using.

Since you dont have access to GWT yet, this would be a good way to see what is going on with this site. You stated that you just started doing the optimization for the client, so you most likely havent had time to research the domains history yet. Once you have access to GWT you will be taking a look at links anyway, so while you are waiting for access be proactive

We went around and around with this question when we rebuilt our site. The conclusion we came to was: We shoud link out to our social profiles and citation links, since they link back directly to us from a trusted network. It was also determined that linking could be helpful, since Google may not have discovered your social network. This was used to jumpstart the discovery of the profiles we had created and further help Google to validate our location and services.

Optimizing and managing 500 different domains is not only impossible under a normal workload, but also will make each site harder to rank.

Like William stated, you are splitting any link juice over 500 different sites. I would focus your efforts on a few domains that produce excellent results, and either let them expire or park them all on top of one domain.

Think about it like this:

Your meta description is a condensed version of what your page is about, including keywords.
Your opening statement is usually about what your page is about, including keywords.

Sometimes you can modify them a bit to add in additional keywords, or to make them more focused on a given topic. To answer your original question, yes it is fine. It is NOT considered duplicate content.

When Matt Cutts is talking about duplications, he means dont have multiple pages with the same ones. Not to avoid having onpage content the same as meta descriptions.

""The way I think of it is you can either have a unique meta tag description, or you can choose to have no meta tag description, but I wouldn't have duplicate meta tag descriptions," Cutts said."

http://searchenginewatch.com/article/2308339/Matt-Cutts-Create-Unique-Meta-Descriptions-for-Your-Most-Important-Pages

If they are truly gone, then a 410 would be the best option for you. Since they are indexed even if there are no links pointing at them, people can still find them besed upon what they are searching for. You never know when your link will show up, because you dont know how long google is going to take to get rid of the links.

http://www.checkupdown.com/status/E410.html 

"The 410 error is primarily intended to assist the task of Web maintenance by notifying the client system that the resource is intentionally unavailable and that the Web server wants remote links to the URL to be removed. Such an event is common for URLs which are effectively dead i.e. were deliberately time-limited or simply orphaned. The Web server has complete discretion as to how long it provides the 410 error before switching to another error such as 404"

We did this for a client that needed old defunct pages removed. Once you set the pages to return a 410, and use Google url removal tool, you should see them dropping off really quick. (all of ours were gone within a month) Having that many pages return a 404 may be hurting the experience of your users as when they see a 404, they go right for the back button.

You can submit them separately. One for video, one for images, one for URL's. This may be a more effective approach at getting things indexed, as it separates them into their own category. If you are already having a high load time, wouldn't hurt to try.

To answer your original question:

"Sitemaps should be no larger than 10MB (10,485,760 bytes) and can contain a maximum of 50,000 URLs. These limits help to ensure that your web server does not get bogged down serving very large files."

But wait, there's more!

http://www.seroundtable.com/archives/021559.html

"Google has changed the number of Sitemaps you can reference in a Sitemap index file. The number use to be 1,000 sitemaps can be referenced in a Sitemap index file, now the number is 50,000 Sitemaps. This is a huge increase in capacity.

Still, each Sitemap file can contain up to 50,000 URLs, so technically 50,000 multiplied by 50,000 is 2,500,000,000 or 2.5 billion URLs can be submitted to Google via Sitemaps."

Google can read Javascript, but only certain types and implemetations. Is there a way you can set this swap out to happen on the database or server side? That might be the best way to get the live text readable, as most likely the javascript is being rendered and displayed after the initial crawl of the page. Even if it is a milisecond later, Google might not allow/catch it.