With taskset on the latency-histogram process the jitter dropped to 0.6. I then moved the six glxgears to that CPU and jitter was 2. I kept adding glxgears until jitter rose to 3, it took four more for a total of ten glxgears.
So, I think taskset is a good thing. The latency-histogram seems to only use a single CPU, but I am guessing that linuxcnc may use more, but I have not tested that yet. I am going to let this run for a couple hours and then document it all (maybe on a more standard Debian install as not everyone grew up writing xinitrc's and running startx).
Thanks for your help, this thread was very helpful.
