Thanks for posting details of your config. Are your data source generating enough data? Just wondering if there are periods where there is no(not enough) data to index, hence you get the periodic large drop in indexing rate.
You have more I/O capacity than my current test bed.
Mine is 64G RAM, 12 core HT Xeons, 2x1TB SATA set up as RAID1 and I have 31 physical boxes running ES 2.1.1. I have 33 separate (same HW config) boxes running logstash 2.1.1 using kafka console consumer, consuming 400 topics into 40 indices. I get a sustained 50K/s indexing rate. It goes between peak of 60K/s to low of 40K/s.
My bulk thread queue is on 100 though. I started with everything set to default and then tweaking one thing at a time to see the difference. This took me from before holiday break to now, about 3 weeks of work
At this point, I think I am saturating my disk I/O, but there is still some room for a little bit more in terms of indexing speed. I've managed to get up to 80K/s sustained for a few hours.