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Have you tried isolating the CPU cores?

I have the same processor, but a different motherboard, and the results are better.

It is possible that your problem is caused by something other than delays, but it is worth trying to improve the result.

 

The E-Stop was cool!

Yeah, where to start looking?
When you turn the servo motor (if possible) and look at the relevant pos-fb pin in halshow, does the pin number count up/down? What value does the lcec.0.xxx.controlword have?
Vendor id and product code from "ethercat slaves -v" match the vid and pid fields in ethercat-conf.xml?
Any error messages from linuxcnc at startup, or errors in "sudo dmesg" that can help?