Taking over a Lion Server

I have just accepted a position in a company that is running Lion Server.  A consultant preceded me, and a quick look at the server suggests that the server was not set up correctly.  For instance, when looking for users on the server to see their permissions etc, I find that the users have not been set up correctly, and you have no access to permissions or checkboxes of any description. 
I suspect the consultant (a PC guy) somehow imported users home directories into the server from their local hard disks, and the screens you get when you access a user are not what you expect to be getting. The file server appears to be running, but they have issues with permissions which are not easily rectified.
So here's my question.  It appears that the server should be rebuilt properly to get the most out of it.  What would the best approach be?  To change things on an item by item basis, or set up a new server from scratch, and get everything correct, and then put that in place.  Or am I seriously confused??
Les

First off, I'm not a heavy command line guy, I know enough to get around and not get into trouble, but that's it.  On the pane issue.  If you "Add User" you get a pane that shows the user name along with a screen that has various checkboxes.  In the server currently in place, the username that seems to be in play appears to be "the short name" from a users local home directory and not the long name that would be displayed had you chosen that fron the list of network users.  For example, if John Smith was a network user, and I chose him in an "Add User" function, he would show up as "John Smith" in my Edit Permissions screen.  If I click on John Smith, I would then get a screen that allowed me to control the read, write etc permissions for that user via checkboxes.
However, what shows up in the list is not "John Smith", but "jsmith" and if I try to do an Edit Permissions on "jsmith" I do not get that pane with the checkboxes, I get something else, a single line of no use whatsoever.  I suspect that somehow the "jsmith" was the home account in a users local home directory and that has been shoe-horned into Lion Server.  I could be wrong, but all sorts of weird permissions errors and things keep arising.
My gut feel is I think we should "start again", and set up Lion Server correctly, but I'm wondering if then putting that in place later is not more problematic than just going in on a user by user basis and trying to replace the bad stuff and get it working properly.  Additionally I have a concern that the piecemeal process would not leave other legacy issues that I'm currently unaware of in place, only to rear their head later.
Any perspective you can add would be greatly appreciated.
Les

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