Hello Keri,
Thanks for a detailed inspection and time spent to analyse it.
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Here, in India - a site with a .com is what is considered generic and is typed naturally instead of country specific .in or .co.in extension. Does having a .com impacts the rankings as searched in India. (Under webmaster - the geogparhical location is set as India only)
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For warnings etc - we do regularly check google webmaster and yes takes very seriously for same. However - if we remove ads (which we learned from some major adsense enabled sites - these are the best practices - for monetizing and ad positioning ) pl suggest if we are doing anything wrong here. There is just one banner ad above the text fold and one link unit
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By building links, 100% with you - but how to build do follow links from external sites - which is the best way to make backlinks - through Articles or other means
Thanks once again for time to analyse and suggest. Hope to get response for above. Thanks