I am assuming this is already resolved now but just in case not, or if you have the chance to change things around.
You didnt mention what storage you had available but I assume from what you said it is stored on direct storage in one of the servers.
I would actually upgrade the 2003 box to 2008 if it will support it, education licensing is pretty cheap so I wouldnt worry about that too much.
With 3 servers you cant really have 2 copies of AD and 2 copies of the user data without causing issues.
If you have a tape backup system use that to make regular backups of the user data which would be stored on whichever server has the most storage available. I would have that server doing nothing but file and print sharing.
With the other 2 servers running server 2008, using the server manager you can install the ADDS role on both servers then run dcpromo on one of them and create a new domain in a new forest. Set up all the users in AD and set their accounts to map their home folder to a share created on the file server.
The dcpromo wizard will prompt you to install DNS, do this.
When you are happy that server is up and running run dcpromo on the final server and add it to an existing domain in an existing forest. This will give you your AD "backup". The final server is where you should set up DHCP as well, and WINS if you need it.
If you have more than a couple hundred machines on the domain, I would recomend you vlan the network off to reduce broadcast traffic, unless you are running IPV6.
Thats pretty quick and nasty but it should do.
If you want to post, or PM me the full spec of everything you have I would be happy to do a full network design for you. Would be good practice for my MCITP and CCNP.