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The tag is to prevent Microsoft Smart Tags from rendering. It was only included in beta versions of IE6, and no other browsers since. It's not worth including; you can safely delete these tags.
An explanation of smart tags on wikipedia.
The same question on stackoverflow.
A lot of items on your home page are getting served securely... which isn't necessary, and will prevent the browser from caching them properly. For example:
Since it's not a secure page, I wouldn't be serving all of these securely. I'd use http:// instead of https://
A good place to start would be to go to the Google Webmaster Tools. If you haven't set it up, I'd highly recommend it. Expand the "Your site on the web" section, and click on the "Search queries" report. The default tab is by "Top queries". Click the tab next to it for "Top pages". This will show all the pages with some information as well for each page, such as impressions, clicks, CTR, and average position on Google SERPs.
I'm not sure if this is a complete list, but it's what I go off of.
I'm not sure why Google's results would depend on how many results you're showing, but if either setting shows a URL, then it must be indexed, right? 
Also of note, if you're interested in getting indexed in Bing too, I'd recommend setting up their webmaster tools as you can submit 10 URLs a day, and up to 50 URLs a month, to be indexed if Bing hasn't indexed your site yet.
One post I came across that could be of interest here regarding Bing. It's a little old, but probably still accurate. It sounds like you could get flagged by them, but only if the number of inbound links suddenly increases by orders of magnitude in a short period of time. Here is the relevant part of the article:
Going unnatural
So what does it mean to go unnatural? It means you're trying to fake out the search engines, to try to earn a higher ranking that the quality of your site's content dictates as natural through manipulation of search engine ranking algorithms. This chicanery can range from relatively benign but useless efforts to overly aggressive promotion to outright fraud. And as the major search engine bots are continually crawling the entire Web, we see what is being done, the relationships between linked sites, the changes to links over time, which sites link to one another, and so much more, we account for these cunning behaviors in our indexing values applied to those pages.
Examples of potentially conspiratorial hocus-pocus that might be perceived as unnatural and warrant a closer review by search engine staff include but are not limited to:
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