Since you are looking for any and all suggestions, one might be to set each indexer up as a cluster of 1, then configure the search head to search across multiple indexer clusters this will work for multisite.
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Take a look into multi-site index clustering. You should be able to set it up so that your data will replicate in both locations, this will not incur any extra charges as it will only matter what data is indexed, not how much is replicated.
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Do you also have the TA installed?
The way I have understood it in the past is that the search head application will lay the groundwork for the indexes, sourcetypes, etc. No data will be populated in those areas until the TA puts the proper props.conf in place. Hope that helps.
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