general setup question - standard cnc process

Dear everyone, i have posted about my cnc issues and am kindly asking for help here   but i think this may become harder to find then i thought. Any tips if there is consulting help or physical help and an option, please do not hesitate. I am happy to spend a dime. 

BUT i am preparing myself for a week of CNC evenings and nights as this is ultra urgent to fix for me and my small shop. 

I am using a mesa MESA 7I76EU STEP/IO STEP DIR plus I/O controller card on my CNC. its about 1.5m X 1.2m with 35cm Z axis travel distance. 
Sadly i was not able to perform the full retrofit fully myself due to time constraints. I did though the complete electronics overhaul. 
I have added a new tool length sensor and a 3d probe. 

From my cnc workflow so far i have this process in mind and I would love your take on it. I have used multiple CAD / CAM solutions in the past, the longest i have used fusion360 and right now im trying out onshape cam. 
But in general the workflow was the same:

1. CAD design the part
2. In Cam I am creating a setup
3. I create and define stock (if necessary)
4. or I set up the part reference point 
5. that defines the WCS XYZ 
6. This allows the postprocessor to generate toolpaths.
7. Using the postprocessor to output G-code
8. I load whatever CNC program (right now linux CNC QT Dragon)
9. I home the machine (if necessary) 
10. This sets G53
11. Then I either do this: 
12.  A) I insert Tool 1, measure tool 1 at the tool lenght sensor. G43 H1 mit Z20 z.b. . Then I take my tool length sensor, place it on top of the material. I am zeroing Z-height (G54 Z = new coordinate - tool length sensor dimension)) and i place the machine head roughly where i want to cut
13. I take a 3D probe, probe the stock or piece or reference that i need. I align the WCS to it. (if the probe needs calibration, i probe the table or a defined height of a pin right next to the tool length measure.) This sets G54 XYZ. Then I insert Tool 1 and measure tool length on my tool length sensor. G43 H1....
14. Run
15. Tool change
16. Measure T2 G43 H2 is stored
17. continue and repeat

BUT it seems that in our setup of linux this process does not work at all. I am getting homing error and out of probe errors the moment i am doing the basic qt dragon features for probing and sensing.