I believe the current progress is pretty much relevant to user but do provide the option to change the location if user want to manually change it! (it will be a good user experience)

To get all links crawled by search engine, here are few things that you should consider!

• Make sure sitemap have all links appearing that have on the website. Including all the links in the xml sitemap will help Google to consider those pages
• Point links to all location pages. This will help Google to consider indexing those pages and make it rank for relevant terms.
• Social Signals are important try to get social value of all location pages as Google usually crawl pages with good social value!

I think the current approach is awesome just add manually change location option if a visitor wants it.

Depends, If you have secure login system on your website then you cannot put 301 on https because in that case user might not be able to access the login area.

Adding canonical is fine and you can also restrict from crawling by adding it in to Robots.txt file.

There is no BIG problem if you add the pages that contain cross domain canonical tag on them. Why?

The reason why I can say this is because Google is not only indexing the pages from sitemap.xml file, Google have their own crawler and they have the ability to crawl and index the website no matter if you do not have an xml sitemap.

Google is very good at (in my opinion) picking the instructions that are available on the page so if you add the page in the xml sitemap, the crawler will read the instructions on the page and will only index the page that contain original content.

Its simple…

Redirect 301 http://www.mydomain.com/index.php to http://www.mydomain.com and all your link juice value and traffic will move to the index page you want and duplicate content issues will be resolved!

Hope this helps!