setuid (and other) permissions lost when copying / elsewhere - what to do?

I sort-of-cloned an existing Debian 7.x distro by copying the contents of the root filesystem (not the special dirs of course) to another HDD. I booted, things seem to run, but - I get some weird errors. One of them - sudo and su wouldn't run, complaining about lack of a setuid permission for the binaries. Well, I fixed that, and now they don't complain, but - maybe there are other files whose permission has been screwed up during the copy? Is there someway to verify and fix all relevant file permissions?