I've increased my index.mapping.total_fields.limit from 1000 to 2000 and confirmed the changes:
"my_index" : {
    "settings" : {
      "index" : {
        "mapping" : {
          "total_fields" : {
            "limit" : "2000"
          }
        },
...
However, I am still seeing errors, albeit less frequent "Limit of total fields [1000] in index [media] has been exceeded". My suspicion is that the error message is incorrect. Can someone confirm this? I'm running 5.5.
Thanks,
Scott