I'm not very familiar with es.nodes.path.prefix, but it sounds like there might be two problems, right?
(1) Somehow es-hadoop is swapping the prefix and port as you describe in Prefix and port appear flipped in es-hadoop implementation - #3 by petersedivec. It would be good to get a ticket for that (with steps to reproduce)
(2) It looks like maybe your elasticsearch is not configured right, since it is failing on curl -u "username:password" --head https://server/es/indexname. I would assume that es/ would have been stripped out of the path before Elasticsearch got to it.