I found an unusual way to cause Kibana to have these timeouts. If I start elasticsearch.bat in a cmd window and select any text in that window (even just clicking on a single character) that blocks Elasticsearch from logging anything and blocks the whole process. From that point on, Kibana will hit timeouts. Is it possible your cmd window is blocking Elasticsearch ?
The exact timeouts you see logged would depend on where Kibana was in the startup process when Elasticsearch got blocked.
Lee