If you can perform the move during a time that the databases are static, perhaps on the weekend, you can temporarily shut down the SQL Server Agent service(s) that are running the replication jobs. Alternately you can drop replication, perform your moves, and then re-establish replication following the database file moves.
For non-system databases, the general procedure is:
1. Take the database offline
2. Copy the files
3. Update the system catalog using ALTER DATABASE statements, for example:
ALTER DATABASE myDB MODIFY FILE (NAME = LogicalName, FILENAME = 'D:\DATA3\PhysicalName.mdf');
4. Bring the database online
For system databases, follow the procedures in BOL or here: http://msdn.microsoft.com/en-us/library/ms345408(SQL.90).aspx.
If you have a large number of file to move, you may find it useful to write some dynamic SQL to generate your ALTER DATABASE statements as well the batch files to perform the copy.
Hope this helps. I regret that I cannot answer any clustering-specific concerns.