My site had been hacked. I found vulnerability,fixed it, and removed shell scripts. But hacker had uploaded thousands of web pages on my web server. after I removed those pages I got over 4 thousand "Not Found" Pages on my site(All linked from an external free domain and host which is removed now). Also hundreds of Keywords had been added to my site. after 3 weeks I can still see keywords from removed pages on my Google Webmaster Tools.

I had 1st result on google search for certain keywords but now I am on 3rd page for the same keywords. 50% of my traffic was from google which is now reduced to 6%. How can I fix both those "Not Found" pages problem and new useless keywords? and Will it be enough to get me back on first result on google?

P.S: 1)Both vulnerability and uploaded files are certainly removed. 2)My site is not infected, checked on google webmaster and a few other security web scan tools. 3) all files had been uploaded on one directory so i got something like site.com/hacked/page1.html and site.com/hacked/webpage2.html