Sal, I've heard that caution a lot, and don't get it. On an uninstall/reinstall/repair, Acad won't touch anything other than the filenames that it installed. If you modify a standard Acad file, it will be overwritten on a reinstall or deleted on an uninstall. But if you put your own version of a standard file elsewhere, not in a standard folder, the uninstall/reinstall will leave it alone, whether or not its folder is located below Acad's. If I uninstall, Acad will leave my folder tree intact in an otherwise empty Acad folder, and report that there were things it couldn't remove.
Our customizations change a good bit with every upgrade anyway. During a transition period, it's easier for me to maintain two separate master copies of our stuff temporarily than to try to make every little thing compatible with either versions. Once everyone's up to speed, I don't support the old version any more.Till now we've done standalone installations, but 2006 willl finally force a network license setup and I'll probably go to a centralized net setup of our customizations.
Reading all the stuff that folks go through with the network install, I tend to think that the old fashioned standalone approach was a good bit simpler. On the server I keep a read-only master copy of our customization folder tree. It contains all our help docs, including a "how to install" memo, our default profile, and several configuration files related to printers etc. An installation consists of : install Acad with all defaults, drag the custom folder from the server into the Acad folder, and import the profile that comes with it. Done -- takes no time at all.
For regular maintenance, I use an acad.lsp which loads once when Acad is started. It checks the local folder tree against the network master, and downloads anything that's more recent or wasn't there. If I change the menu, I simply post a revised mns (not mnu) and it will get downloaded and recompile automatically as the first drawing loads locally. That was one advantage of mns over mnu -- you didn't have to force a recompilation. All I do is send around a memo saying you might notice such and such changes have been made automatically.
When we go centralized, I'll probably keep the working copy of our stuff in one location, and a backup master copy somewhere else, read-only. I may still put the "user" folder (in which people are allowed to customized a personal partial menu) on the local machine, since it's the user's responsibility to maintain.