i dont remember if 2008 supports legacy mode for domains ( eg old nt4 domains) if so just run your domain in that mode and you can still have your devices connect to that domain
now if it dosent you can create local users on a machine that is part of the domain and and have the same login credential /users as the win98 and it should (in theory) work . ( long time i havnt adminsitered any networks)
to communicate with each computer you dont need to be part of the domain juste need to have ip setup if you want to share files just setup a ftp server on a machine and then you can connect to it with just about any systems XP can join any domain with AD . both native and legacy mode . there is always the linux that can be had for older machines but its more complicated ...
there are also other software that uses ip to sync stuff up.
Edit : you dont need to be in the domain to connect to a server in it , you can just connect a share and save the credentials . and possibly run a vb script to sync it all up ...


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