The thread on the Elastic discussion boards you’ve linked to already shows how to increase the maximum number of fields per index/mapping, also see https://www.elastic.co/guide/en/elasticsearch/reference/5.5/mapping.html#mapping-limit-settings for details.
This being said, I think having 1000 different fields in one index is a bit excessive and you should think about splitting up your messages in different index sets, so that each index has less than 1000 different fields: http://docs.graylog.org/en/2.3/pages/configuration/index_model.html