So I've used Cerebro to get a better overview of the issue. I can now watch the JVM heap size on each node slowly increasing to sometimes 90% on one of the nodes. I can see that I have 42,087,876 docs, 1782 shards spread across 3 nodes and a total size of 58GB, each with now 4GB of JVM heap. Based on the above, can you confirm that the reason I am seeing all these timeouts is down to the sheer number of shards/docs?
If this is the case, what are the steps to reduce them? I only have 179 indices. Is it a config issue that I've screwed up on the initial build?