Trouble having my pages indexed

Hey folks,
I own a site and have been working on it for sometime now. Some of my pages have already been indexed by Google. A couple of weeks back; I got a message saying that the site can affect my system. I tried convincing the host provider, to check the site and clean the virus. The site was not online for about a week. Then however, Google reconsidered it, and the message stopped appearing. But Google is still not listing a couple of pages for the keywords. These pages are missing on the Google search too. How do I solve this problem?
Thanks for the help

See original post by nikonjems