You need to have multisite = true on the search head. It's confusing based on the server.conf.spec because it says it used to inilizae the master. However, this needs to be on your search heads and Cluster Master. Not your indexers. The Site= Site1 needs to be on the indexers. But the search head config needs the following:
[general]
site = site1
[clustering]
multisite = true
master_uri = https:/A.IP.Address:8089
mode = searchhead
http://docs.splunk.com/Documentation/Splunk/6.2.3/Indexer/Multisiteconffile
... View more