I think you have a couple options.. the way you are suggesting is not the way I would do it. The server consolidation wizard won't move your users, groups, etc. It's main purpose is to consolodate storage space.
1.. Use the Migration Wizard.. It takes your current tree/server and plops it down on the new NW6.5 server. Works pretty well, most of the time. File copy isn't the best but you can do that manually and still proceed. With this method, you may have problems with the LDAP which will break the web interfaces, but is easily fixed after the fact.
2.. Install the NW6.5 server into the same tree as the NW5.0 server. It will get a replica of NDS and so it will have all user info, etc. Then Use the Server Consolidation wizard to move files and trustees, etc. After you're done, take the NW5.0 server out of the tree. The key piece here is that your NW6.5 server will get all the NDS info from being in the original tree and receiving a replica of NDS.. Then the server consolidation wizard will move stuff over and should retain the trustee file assignments.
In either case, you should get your NW5.0 system patched fully before proceeding. This will ensure you have the latest NDS code and less compatibility problems during the transition.
Marvin Huffaker MCNE, CNE
Marvin Huffaker Consulting