After setting repFactor = 2 at the default level and running with that for awhile, can I now go in on a per indexer basis and set repFactor = 0 on some indexers so that only a few are replicating at a time and I can phase in index replication?
No. The repFactor setting must be the same across all peers in the cluster. All cluster peer nodes must set repfactor=auto for all clustered indexes.
See http://docs.splunk.com/Documentation/Splunk/6.5.1/Indexer/Configurethepeerindexes
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Replication factor two means the cluster maintains 2 copies of all raw data, not that all indexers maintain a copy of data separately. Any specific reason you want to have some indexers not take part in replication (or not be part of cluster if they are not replicating)?
No. The repFactor setting must be the same across all peers in the cluster. All cluster peer nodes must set repfactor=auto for all clustered indexes.
See http://docs.splunk.com/Documentation/Splunk/6.5.1/Indexer/Configurethepeerindexes