[TYPO3-english] typo3 6.1.3 not working properly and not upgrading after malware attack

[jeetu dubey]

I have a typo3 v6.1.3 which was recently attacked by a malware. although, we had the malware removed but the site is not working properly after that. 
miscellaneous bugs occurring randomly.
I even tried to upgrade it to 6.2 LTS through manual update but still no luck.
I also did a fresh install of 7.2 LTS in a subdirectory on the same server & it works fine.

thanks
Jeetu