I think all the implementations work just about the same.  We chose to do it in our sitemaps because that was the easiest for our developer to implement.  You should choose one or the other, there's no need to do multiple implementations.

(This is all speculation as I've never done this before.  There are probably people in the forum that have)

Be aware you're switching from a ccTLD to a gTLD.  Is the clinic primarily for Canadian residents?  In the simplest terms, switching from a .ca to a .clinic may hurt your Canadian rankings, and help your rankings everywhere else.  If you want your site to continue targeting Canadians specifically, you can set that in your Google Webmaster Tools, although I think having the .ca domain itself is a stronger indicator to Google that your site is geared towards Canadians.

It sounds like Martijn solved your problem, but I still wanted to add that robots.txt exclusions keep search bots from reading pages that are disallowed, but it does not stop those pages from being returned in search results.  When those pages do appear, a lot of times they'll have a page description along the lines of "A description of this page is not available due to this sites robots.txt".

If you want to ensure that pages are kept out of search engines results, you have to use the noindex meta tag on each page.

For geo-redirects, I do not recommend you use 301 redirects.  Browsers can cache these, so if you tell a browser in Canada that example.com should redirect to www.example.com/ca-fr, and later the user changes their language to English, and then tries to go www.example.com, the browser could use that redirect again to go back to the French version without hitting your server.  301 tells the browser that www.example.com ALWAYS (permanently) goes to www.example.com/ca-fr.  Page rank isn't really a consideration with these, since Googlebot always comes from the US, so it should never hit these redirects.  If example.com always goes to one of the versions via a redirect (i.e. you don't serve content under that root URL), then you do have a bit of problem with redirects.  You don't want to 302 Googlebot to another page for your home page, but at the same time, you want to avoid weird redirect behaviors for your customers.

Google can visit the international versions directly without redirects, right?  They should have no problem indexing those pages then.

I agree with István, get some local links to your different local versions, register them each with Google Webmaster Tools (and Bing), put up sitemaps for each, and implement the hreflang tags in your sitemaps (or pages).  That way Google can easily index each version, and knows exactly what each version is for.

Weird. We were having a problem where lots of our skill pages were getting our

<noscript>text used as page descriptions on Google SERPS.  We added these comments, and Googlebot reverted to using our meta description as the page descriptions in SERPs.  It could have been a freak coincidence that Google stopped using our <noscript> text right after we implemented the tags, or possibly Google was (possibly accidentally) supporting them for web search awhile back when we originally did this, and now has stopped supporting it.  Anyways, our SERPS remain clean of our <noscript> text today (<a href="https://www.google.com/search?q=site:www.ixl.com/math/grade-5" target="_blank">example</a>).</p> <p>John Mueller recently commented on that Quora thread saying it won't do anything for web search, so IMO that puts this to rest.</p></noscript>

You can set up the goals in the subdomains profiles if you want to view goals there.  That's entirely up to you.  Each profile is its own thing.  When I say "filter", I mean write "example.com" into the search box there, and search by it.  You can also click "advanced" next to the search box, and make the search more granular if needbe.