Thanks for the tips, I'm not sure what I was seeing before... I ended up restoring a filesystem snapshot, checking using the elasticsearch-migration plugin for 2.x, going to 5.x, starting elasticsearch and waiting a long time and eventually it came up, then installing x-pack in elastisearch and kibana, starting elasticsearch and waiting a long time (it complained about .watchers stuff but eventually got over it). Then I started Kibana and now I'm able to use the reindex helper to slowly reindex the 196 indices. Phew. I think the biggest thing I did was just letting elasticsearch work through whatever problems (.watchers etc.) it encountered as it was coming up even though it was throwing ERROR log lines.
One big thing that confused me as I switched versions was the
path.data settings in
elasticsearch.yml. In 2.x it expected the path to be
/foo and in 5.x it expected the path to be
/foo/elasticsearch. Don't think I saw this documented in the breaking changes.