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after editing the PNCCONF according to kworm - update 
forum.linuxcnc.org/39-pncconf/56464-mesa...thcad-pncconf-screen

is possible to configure the step-dir spindle in 7i95T

Could you post the G-code that is giving the error? Not necessarily the the entire G-code program. Especially if the program is large. Just a snippet that includes at least a few lines before the error, and a few lines after, so we might be able to test and reproduce the error. It's a little hard to see and understand what is going on just from your image.

The error joint2 limit error is not caused by your hal or INI settings.
It results as it tells you, because the movement in line 11 will exceed the soft limits.

As you mentioned, that will happen more often with long tools, as your code will use a length compensation for tools.
If the preview window is updated, you will see that limit violation too.

Try the following:
- Change to the longest tool.
- set Z axis to cero on the top face of your workpiece.

Now it should work. 
 

I did a complete re-install and made sure I selected the right board starting config, and now everything works as normal. I must have accidentally started with a tangBOB starting config instead of the TangNano9K, or something along those lines, so as I was re-installing linux/checking hardware I brought the problem along with the original JSON file every time I tried fault finding.

If nothing else I can serve as a bad example !
Cheers.
Russell.

160i is what i recall from the naming on the console, it was made in 2012, again i think, as i do not care much about such info when tasked with making such things work.
I will update info whenever i get a chance, as the stress is gone so now i might also do a less shaky video.
I said "i might" ...