The problem is bit unclear to me.What do you exactly want to check in the passwords..?
If you want to check if the user exists on thousands of servers , then one hint is to use ssh and check the /etc/passwd file on all servers for those particular users.
Meta answer - use expect scripting language, or its child - autoexpect - look at the man pages for both, they are very useful when automating unix passwords or similar tasks.
I take it that your root passwords are different is to why you want to even do this. With that being said you may have to log in to each server anyway.