My site had been hacked. I found the vulnerability, fixed it, and removed shell scripts. But the 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?
- Both vulnerability and uploaded files are certainly removed.
- My site is not infected, checked on Google Webmaster and a few other security web scan tools.
- All files had been uploaded on one directory so I got something like