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I would still appreciate knowing how to call anyone of these routines without going through the entire program.

You can call any subroutine in a loaded program from MDI (eg 'o100 call')

Also how to set the Z after the tool change.

Do you mean the tool-length offset or the work-offset?

The currently active work offset can be changed like this:
'G10 L20 P0 z123'

What about the "rawcounts"? when i quickly had a look at them in halscope they seemed to have "0" at a fixed location, do you think that's something i could use in some way?

Is dist-upgrade ever a good idea?

Yes, when you download an ISO, it might be several months old, so that will update to the latest stuff for that distro, including kernels and stuff that "might break things".