vpopmail/qmail/freeDSB/Compromised server/problems

okay so, we have a server that got hacked into by a stupid user not using a good password. They did all kinds of garbage to our server, and my boss just did a changemod for the whole home/vpopmail directory to lock it down, and now the mail isnt' working at all (hasn't been for 2 days and people are getting angry) we are sure that it is just a permissions item, but we don't know where to look hor how to fix it. the errors in the logs we are getting are..
mail inetd (25125) : cannot execute /var/qmail/bin/tcp-env: permission denied
_secure_path: cannot stat /var/qmail.login)conf: permission denied

We are getting those over and over and over... I am workingas an internship right now and something like this could make me get a paid internship, and make it so that I could be getting paid, and making it so that we could keep our house...

Please help me so I can keep my house... (woooha guilt trip!)

Well here's a list of the default should-be permissions:

/var/qmail:
nske.rootforge.org/temp/qmailpermissions.txt

/home/vpopmail:
nske.rootforge.org/temp/vpopmailperm.txt

But if they are really messed, perhaps it's easier to just delete everything and reinstall?

that helpped a lot thank you.