This only a problem for some product but not others.

Are these "some" products have specific names (language, special characters ...etc) or anything different from other products?

Hello.

Please separate your questions. One question = one topic. This help other with similar issues.
For the SSL problem do you have SSL certificate installed? If it is not installed or have issues than browsers block by default this connections as not secure

Some product descriptions had HTML code in them, could that be messing it up?

Well storefront show html on product pages and listing list view, so if html structure is broken this may cause some issue. You can post your html here so we will check on our side

Any suggestions??

Hi. Few suggestions:
1. Go to Admin > System > Localization > Language definitions and remove this definitions. Then add definition again and clear cache.
2. restore backup and try to upgrade again

Actually you can use Excell but it not show delimeter wizard when open so you need to do this in another way
In my excell version I need to open Excell then choose Import select my file and wizard ask about CSV parameters. If just double click and open CSV excell do this wrong way. 
http://superuser.com/questions/407082/easiest-way-to-open-csv-with-commas-in-excel

Hello.

gzip compression it is something about your server configuration. If your server allow gzip compression please also enable default AbanteCart .htaccess file https://github.com/abantecart/abantecart-src/blob/master/public_html/.htaccess.txt

For the sitemap take a note there are two sitemap types:
1. Sitemap page for your customers http://demo.abantecart.com/index.php?rt=content/sitemap
2. XML sitemap for search engines you can generate it manually (just google it) or install extension with xml sitemap autogeneration which is better because your site changes mirrored in xml sitemap automatically

Hi.

Thank you for reporting issue. We will improve this in next version

Hello.

To do this your need some html and css skills. To find where is footer block located check this tips http://docs.abantecart.com/pages/tips/template_debug.html