Upgrading Mac OS X Server 10.6 to Mac OS X Server 10.6 to fix issues

I have a new XServe that was migrated from a G5 10.5 Server. Mac OS X 10.6.2 appears to have caused some issues which I did not realize until I attempted the 10.6.3 upgrade which utterly failed. It appears that 10.6.2 is not running many cli tools and in 10.6.3 I have found the entire var dir at least is incorrect. Tools in 10.6.2 that are not working include locate, ln, and man if not more.
I would like to reinstall. This server is bound to a AD server and I have read that you can upgrade 10.6 server to 10.6 server so I wanted to verify this as it would be the simplest way for me to do this.

I made a clone of the server boot drive and ran some test to see what was possible. This can be easily done by erasing a drive and then installing a fresh Mac OS X Server 10.6. Upon reboot supply the serial number and then it will ask to migrate the data and you can choose the existing install (in my case I had one clone with 10.6.2 and one with 10.6.3). After this I tested to see that the OS was in good shape unlike the 10.6.2 which was missing key unix functionality (man, ln, and others). I then updated with the Combo updater to 10.6.3 v1.1 and all was well.

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