Migration of Wordpress MU

Dear Expert,

I need some help and advise.

Currently I have a Wordpress MU site included in a http://www.domain.com/home/ using some custom script. We have about 300 over users now.

We wanted to a upgrade of server and also change of domain name.

What plugins or script can we used to backup, clon our entire site to a new domain name http://www.newdomain.com and this time we want run without the sub folder.

What file we need to take note and any expert that we can outsource this entire process to ?

We do not want to affect our member sites too much.