I just wondered if anybody could help me with a few configuration convention issues for sitemaps, canonicals and indexes etc?

I have written a website using PHP, and use an .htacces file to rewrite all .php files to .htm.
Also, had to redirect old page links to new locations, as all the page files were located in the root, now each page is located in a separate directory.

Q) Should the sitemap reference the original .php or rewritten .htm web pages?

HTML Code:
<link rel="canonical" href="http://www.***.com/index.htm"/>
<link rel="index" title="***" href="http://www.***.com/index.htm" />
Q) Should the HTML code above reference .php or .htm?

I only as ask because after a month, Google Webmaster Tools hasn't index'ed the new links, but the new and old .php links are viewable in Google.co.uk

Thanks for any help,