Transferring Files After a Clean Install
The short answer is that there is no easy way to know what files have been corrupted and what impact they may have.

The best solution is to rely as little as possible on the files on the old backup. You have made a good start by doing a clean OS install. Now re-install all applications from scratch, preferably by downloading brand new installers. Once you have done that then get all your documents, music and other data files from the backup but not such things as your Library folder. Thi means you will have to set the preferences on all your applications again.

This is a lot of work but the safest way to do a clean install.