Manual Tool Change Error

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. 
 

Maybe try making a new config in pnccomf and see if you can get that to work.