File organization

Hello my fellow MGers. I come to you in need of advice again.

At work we are rebuilding our file server into a virtual one and my boss would like the directories organized better before we do this. In the past, users have had full control of the folders and they've created a giant mess. The biggest issue we have is that they've created a folder structure so deep that Windows and our backup software can't handle the path lengths. Added to that, permissions and file ownerships are right out of whack as well.

Can anyone recommend a program (if one exists) that would help me organize our file server and especially fix our path length issue. To go in and change things one at a time by hand woiuld take ages.

Thanks!