Out of your services (AFP/SMB, Mail, OD, SWU, and web), the one with the most potential for disaster and headache is clearly mail. If you are using the same host device, cutting services over in pieces will not be possible. However, here are some suggestions and potential points of concern.
AFP/SMB file services are cake. The only thing you need to consider is the potential time to copy the data if you are moving it to new disks. The other issue will be user's GUID values and the associated ACLs. Let's take the following scenario based on what you've detailed.
• You have data on /HDD/Shares/ and you are planning on moving them to the SSD. Is the SSD drive large enough to accept this data?
• If you had a share /HDD/Shares/Data and this contained an ACL allowing the design group to have access, the design group from the 10.6.8 OD may have a different GUID than the one you create on the 10.9.1 system. If this is the case, you can purge all ACLs with a sudo chmod -R -N /path/to/data. (Server.app should remove and then add but older versions resulted in merged messes so I go nuclear on the old settings) Then you can apply your new ACLs and allow the permissions to propagate.
• If you are leaving the data were it is, you will simply need to reset permissions. However, note that if you are exporting and then importing users (via an OD backup or via standard record format) then you are maintaining GUID and should not need to touch any permissions.
Regarding SWU, I would suggest looking into Caching server. If you are moving the entire environment to 10.9 and iOS 7, SWU is no longer needed. Caching server is easy as pie, requires no client configuration, and is more economical on your internet connection and server storage requirements.
Web is pretty easy also. But, this is dependant on what you are doing with web. If html/php/perl then you pretty much just move your site folders and you are up and running. If you were using MySQL, note that Apple replaced it with Postgres. You can either perform a conversion from MySQL to Postgres or you can just install MySQL again manually. The choice is yours. If you are not doing database backed sites, the migration should be cake.
OD is one of those technologies that I always prefer to start clean. In really large environments, this can be very tough due to passwords. You can export an OD backup from 10.6 and attempt a restore in 10.9.1. If you have a lot of MCX in 10.6.8, you may run into some trouble as Apple has deprecated MCX in 10.8 and above. However, this ensures that you have everything, from password to GUID. Test, test, and test some more if you go this route. An alternate option, especially if you are embracing the move away from MCX and to Profiles, is to do a user and group export for 10.6's Workgroup Manager. This will not provide passwords but it will provide editable text files of your account data. You can strip out the MXC and other legacy values and then use the resulting file to import users into a clean 10.9.1 OD master. Once again, you will not get passwords unless you add them to the import file. You need to figure out how many accounts and how sensitive users are to password resets.
The final piece is mail. This is the one area I have very little experience. I've been burned by Apple's mails solutions from way back in the AppleShare IP days and now make it policy to use anything else but Apple's mail solution. In a perfect world, moving the mail data store to the new OS and triggering Server.app should be enough. But Apple + mail never seem to enter the realm of a perfect world.
And finally, make sure DNS is correct before you do anything. Since you are dealing with mail, you should also shut firewall port forwards to prevent new mail from coming into the server while you work on the migration. Nothing worse than stitching mail together after a blown migration attempt.
R-
Apple Consultants Network
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