I am sure this is a common topic but I couldn't find exactly what I wanted to know. I have had a webstore up for 2 years now but it was utter crap and was poorly indexed.
So we created a whole new site and have that live now and it is being indexed very well to start by google.
The current issue is that google is showing 818 pages in the not found section of Webmaster tools, these are all from the old site. They are all "404 (not found)" and the number is has grown from a few hundred to this. I am wondering if I these pages will be unindexed shortly or if I need to do something more to make speed this up.