Thanks All,
The issue with the lower traffic keyword is that the main keyword I was ranking for was receiving 20k avg. monthly searches and the new keyword receives 50 searches (using the keyword planner tool). So you can imagine, I used to be position #4 for the prime keyword, now I'm #19. So my traffic has dropped significantly.
My homepage uses the www, I used the site:www.mysite.com and my homepage does not show up, I have 57 results and have checked each SERP. When I use the site:http://mysite.com, my homepage shows up as the first result.