Get your hands on a copy of 'Hardening Apache' by Tony Mobily click here
It's the only title I'd suggest being worth the money to buy and the time to read.
It's been a while since I last fooled with Mandrake. One of the things you have to keep in mind is that although there are common areas between distributions, there are also some very real peculiarities between some of them.
You've asked some huge questions in one, so here are some ideas for you:
Most rootkits mimic the creation dates and file sizes of the original system binaries. Rather cleverly (you have to admit) they do this while replacing them with infected versions.
Sysadmins sometimes calculate the cryptographic checksums of vital files and store this information in a safe location, such as on a CD which cannot be overwritten.
The best way to lock things down without going into a huge and very boring discussion of the various possibilities involved is to use Tripwire click here
Tripwire automates the process of checking file checksums and has lots of options for live monitoring, alerts and so on.
NOD32 is my overall favourite for all platforms. F-Prot and F-Secure are worth a look. Any web search will return several worthy alternatives.
I don't understand your question on CHMOD for users/groups to 'allow Apache to run smoothly'. That's not how things work and a re-read of the documentation for both Apache and Mandrake should serve as a good starting point.
Not sure why you'd want to set this one up to begin with.
Would you mind letting me in on your course ?
No offense intended, but you seem to be wrestling with some of the more horrific aspects of server admin without as firm a grasp of the fundamentals as you might have. I hope that didn't come over as an intensional insult because that's not what it is meant to be. With a better grasp of some of the more basic elements of Linux web server configuration many of your questions would become redundant. As a lecturer I don't like the idea that you might be in at the deep end without sufficient preparation.