Custom large scale 4 axis wire cutter and a retrofit of an existing CNC

Hey everyone, 

1.5 years ago i bought a CNC mill. It was a used portal cnc (barely used) with chineese base and german splindle, table, controller and linear rails upgrade by a manufacturer in Germany. It was based on CNC Graf and I always had issues with it. Either Fusion to cnc gcode was faulty, did not execute all commands etc. etc. etc. 
I grew and also wanted to build a large scale foam cutter for 1:1 RC plane replicas. So i said its the perfect time to retrofit the old cnc and to build the new 4 axis foam wire cutter and build it with linuxcnc and on the base of mesa7176EU. 
I bought all parts for the wire cutter and some upgrades for the existing cnc (touch probe, hand wheel, two tool measure sensors). 

This is the wire cutter design i made. 
https://imgur.com/a/XOdKh2n

I had so many issues even getting linuxcnc up and running for the mesa ...  Of course due to my limited experience with debian but also since there are so many unknowns on the mesa world as well.
I thought I will share my project (s) here and also post the wiring diagram and the configuration as i am continuing. 
Right now i finally got the motors spinning and hal machine enabled properly and am working on setting up the limit switches for the axis. 

The first questions that are right now open are in this direction. I will post later the configuration right now for the portal CNC. The wire-cutter is build in parrallel but priority has of course the retrofit of the portalCNC to get at least one thing back online. Wirecutter:

1. How do I configure multiple Y and Z axis in axis configuration for wire. I have two L legs basically so i need to control 4 Axis. In the linuxCNC setup i only saw the configuration for the XZY and XZYA. It should in the end basically have two heads .

Portal CNC

1. We have NPN NO sensors and are connecting them to a mesa board that has “sinking inputs”. I understand that a pull up resistor is required for it to work, but is it the “good way” or would it be better and safer to use a PNP NC Sensor.  Bear in mind that our sensor is a limit and homing switch for each axis. And if a pullup resistor is okay to go with, then will the difference between 2kOhm and 10kOhm  be important for accuracy ?
2. Stepper driver DM556 ENA+ and ENA - with mesa 7i76eu.
   The default for them is to be left not connected when using different controls(STEP+- and DIR+-), but are there any long term downsides to it? any way to use them for improving safety of cnc operation.
3.  If I understand correctly, reversing inputs/outputs in HAL makes changes operational only when the linux cnc terminal is operational and connected to the mesa board, in any other state the outputs will be “as they are” not “as set up” ? Or some of the configuration (In systems like(PC(Linuxcnc) - ethernet - mesa) is stored on mesa? If so, then what are the good practices about what should be done hardware wise and what can be safely done software side.

1. Suggested pullup is 2.2K 1/2w for 24V. The only disadvantage of the pullup is the wiring nuisance.
10K will not work.

2. Enable on simple step/dir drives is not of much value safety wise as it's very unlikely to have a runaways
without the control generating step/dir pulses (and step generation will stop on a LinuxCNC or communication fault)

3. Its important that the default state of 7I76EU outputs be the safe state as all outputs will return to the power up state on
communication loss. This initial state is all outputs open circuited (this is true even if the outputs were set to push-pull mode)