I had a few thoughts regarding your inquiry.

Based on the information you have provided, I have made the following
assumptions:
-A trust exists between domain  A and Domain B
-Domain B is a Windows 2000 Active Directory native mode domain
-Global groups were used to apply security to the Web Storage System of
the SPS server  in domain A

You should be able to use tools like NetIQ domain migrator to migrate
users and groups. All users  and groups that are migrated  to the native
mode domain will use the SID history attribute to be able to access the
SPS server in domain A.

As far as moving  the SPS server, I believe that it can be moved by means
of performing a backup in domain A then restoring it in domain B but
might be difficult to manage the existing security of the web storage
system after the move because it might have trouble associating the SID
in the WSS to a common name of the recently migrated users and groups.
It may require that you leave domain A up until a utility exists that
can migrate  the security of the WSS.

Of course, I would highly encourage testing all of this before
migrating.