Thank you,
HI Lucas, I am on IIS so not using a .htaccess but do have a rewrite rule in an ini file.
This is what I have in the rewrite rule:
RewriteRule ^/manager/.* - [L]
RewriteRule ^/assets/.* - [L]
RewriteRule ^/(.*).html /index.php?q=$1 [L,QSA]
So just add your code to this rewrite rule?
And thank you for the point on adding the Canonical meta tags. Would you apply that to the template for all documents, even those that are indexing properly?
Just to clarify, I am staying at the same domain I have had for a long time. After 2 years of not touching the DNS settings, last week Google indexed this domain on it's nameserver. I am on a Plesk panel, I have 2 IP's and all 5 domains resolve to these. Since this domain in question is exclusive one of those IP's, somehow Google started to index the site on the nameserver associated with that IP. Had in not been exclusive I do not think this could have happened. The name servers were in the name of my personal domain, different than this domain indexed wrong. About 1/3 of the links have been indexed now with ns2.mypersonaldomain.org rather than www.domain.com.
I did not have a Google Webmasters Tools account and so just set one up and did the checks you have mentioned. A little new to that aspect. I did not know you could submit this for review, and so I need to find that link, as it does not stand out to me yet. I have had a sitemap, but just now added the sitemap to the GWT account. The site was #1 in the Rankings without GWT, thanks to MODX's fantastic SEO. In Bing and Yahoo which did not index on this link, it is still #1.