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Thanks for the help guys, But I wasn't being sarcastic in my thread title my brain is as smooth as glass. like a surface plate almost so forgive me. Included is my edited postgui.hal file that I have added the commented out parts for the probe and the spindle speed (hopefully I've done it correctly.

And the new error pop up I'm now getting.

comment out the net in the postgui hal I just realized i missed the post gui hal edits i the docs and will add. you may also want to comment out the spindle feedback line if you arent using it or it will be your next error pop up.

You can omit it by adding # in front of the line containing that pin, but that might limit functionality.

Yes! The problem is gone, even without the r8168.aspm=0 and r8168.eee_enable=0 settings. Before I also tried quiet isolcpus=2,3 on its own, and although the latency improved, it did not resolve the EtherCAT servo following errors.

From what I can conclude now is that updating the realtech drivers according to Rodw's document did the trick.

Some additional info. For my implementation, the EtherCAT reading and writing combined takes 14% of the 1 ms servo loop time.
To check that you can get the number of CPU ticks for each with:
halcmd show param lcec.read-all.tmax
halcmd show param lcec.write-all.tmax
Add those together and multiply by 1/CPU frequency, that gives you the total time for each servoloop iteration that EtherCAT requires.

Now I can finally write a detailed update/installation procedure for my customers and release my new EDM components.
Many thanks again! Great way to start the weekend

so does this mean I need to add the pin my probe is assigned to the probe_basic_postgui.hal?

From the error report:

Sorry, hopefully this is better
 

Missing pin in the probe.....postgui file.
Click on "create report" on the error screen, then upload that here, makes it easier to copy/paste exact lines.

I have considered what you said. I also ran update-initramfs but without success.

Das ist natürlich auch nicht eine kontinuierliche Bewegung in XYZ. Du fährst jeweils einen Punkt an (XYZ ändern sich) und dann in der nächsten Zeile drehst du die C Achse an Ort und Stelle, dann fährst du den nächsten Punkt an.

I have servos on both Y axis (gantry style machine with dual Y screws and servos) and X axis. Stepper on Z.
5i25 card driving things. Feels like software since it doesn't loose position. It does pop an error after the move.
<can't do that(EMC_TRAJ_SET_TELOP_ENABLE) in auto mode with interpreter idle>
Not sure if that lends any help. Also I am going to try a different program, I just realized it is also a new program so maybe there is some code that does not belong.

Reading through the error I saw (twopass:CANNOT FIND FILE FOR:custom.hal) line and saw that custom.hal is not in the example so I commented that out in my .ini and get this error log now

Habe nun P1.000 hinterlegt, doch den Eindruck das die Zeilen immer einen Augenblick brauchen zum Laden habe ich immer noch.

Eventuell liegt es jedoch auch daran, wie ich meinen G-Code gestaltet habe.
Hier ein Mini Auszug:
 

Ok, So followed the guide from square one, installed Probe_basic and QTPyVCP from scratch and have the sims working fine, Created a new config using Step Config in Axis and had that working fine...

Followed the guide on Github word for word (At least I think so) and am now getting errors, I haven't changed or added / subtracted anything. this is as it from following the guide. Included in my .ini .hal and the error report and a screen shot of my config folder to see what Files I have in there 

Thanks

Error report created by /usr/lib/tcltk/linuxcnc/show_errors.tcl:

Print file information:
RUN_IN_PLACE=no
LINUXCNC_DIR=
LINUXCNC_BIN_DIR=/usr/bin
LINUXCNC_TCL_DIR=/usr/lib/tcltk/linuxcnc
LINUXCNC_SCRIPT_DIR=
LINUXCNC_RTLIB_DIR=/usr/lib/linuxcnc/modules
LINUXCNC_CONFIG_DIR=
LINUXCNC_LANG_DIR=/usr/lib/tcltk/linuxcnc/msgs
INIVAR=inivar
HALCMD=halcmd
LINUXCNC_EMCSH=/usr/bin/wish8.6
LINUXCNC - 2.9.2
Machine configuration directory is '/home/cnc/linuxcnc/configs/CNCMACHINE'
Machine configuration file is 'CNCMACHINE.ini'
INIFILE=/home/cnc/linuxcnc/configs/CNCMACHINE/CNCMACHINE.ini
VERSION=1.1
PARAMETER_FILE=probe_basic.var
TPMOD=
HOMEMOD=
TASK=milltask
HALUI=
DISPLAY=probe_basic
COORDINATES=X Y Z
KINEMATICS=trivkins coordinates=XYZ
Starting LinuxCNC...
Starting LinuxCNC server program: linuxcncsvr
Loading Real Time OS, RTAPI, and HAL_LIB modules
Starting LinuxCNC IO program: io
linuxcnc TPMOD=tpmod HOMEMOD=homemod EMCMOT=motmod
twopass:invoked with <> options
twopass:found ./CNCMACHINE.hal
twopass:CANNOT FIND FILE FOR:custom.hal
twopass:CANNOT FIND FILE FOR:custom.hal
Shutting down and cleaning up LinuxCNC...
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments

Debug file information:
Note: Using POSIX realtime
2001
Stopping realtime threads
Unloading hal components
Note: Using POSIX realtime

---

 

@tommylight

Home set to 0
Home offset set to -5

 Did that. It go up fast click returns slow click and it goes up again but it don't clear the switch and I get error:

Joint2 on limit switch error
Position: relative actual 
 

And I can't move the machine.  
If I make home offset 

Home set to 0
Home offset set to 5

I get exactly what I want : go up fast click returns slow click and goes it goes down 5 mm buuut .... i get an error :

Exceeded POSITIVE soft limit (0.0000) on joint 2

@rodw

Your first link is all you need.
The chapter on ini configuration may be slightly useful too.
Note that Home switches must stay triggered to end of travel. Are yours doing this?

Thank you! If that all I am screwed because non of this make sense .
If "Home switches must stay triggered" why do i get error :

Joint2 on limit switch error
Position: relative actual 

BR