Retrofit cnc 3axis

Ok, so there is no pin labeling on the drive boards that would have been helpful.

The data in the file ...\MC53\IOPORT.DEF seems to be the port definition for the microcontroller which is also not much help.

What I would do now is follow the individual traces of the two IDC connectors ("Inputs" and "outputs") and see where they go to (ie does the trace go to a drive connector and if so which one) then check if that corresponds to what you already have found (make a list for each connector and it's pins and write down the functions you have found.
As for the spindle I don't really know if there is more to it than turning it on through the pin you have already found and adjusting the speed with the potentiometer on the front panel.

After that I would think the next step would be to wait for the IDC breakout connectors and try out the functions by manipulation of the pins.

which card can I buy to connect linuxcnc with these drives?

Those are step/direction drives but require 12V signals instead of the more common 5V. Also you need quite a few inputs and outputs (although probably not all 24 each) also 12V. Might be worth to start a new thread on this forum asking if anybody knows of a suitable board. Maybe you will have to look or ask around for a convertor board to convert 5V signals to 12V signals.

I noticed that the connector to enable the axes has two wires, can I search for continuity between one of these and one of the pins of the idc 20 output connector?

Those two wires (with the spiral wrapping) seem to go to yet another PCB board (no idea what that is for). So you will need to test the functions of the machine and monitor those outputs to try to find out what those two signals are for. Might just be to activate some power supply or maybe a spindle brake (freno mandrino) that is mentioned in several places in the documentation.

should I see the pulse train on the transistor pin when I activate its function?

On an oscilloscope, yes. Although I would ask around for a suitable breakout/convertor board with 12V input output first.

I'm dreaming of the damn pin that enables the axes.

The enable pin(s) will have a trace going to each of the drive connectors on the drive connector pcb but since there is no documentation on the drives it might not be so easy to find the right ones. As I mentioned before there might be one signal from the output connector that is split to all the drive connectors or separate signals for each drive. 

I want the penguin xD 

In your case the penguin wants to be earned

Those two wires (with the spiral wrapping) seem to go to yet another PCB board (no idea what that is for). So you will need to test the functions of the machine and monitor those outputs to try to find out what those two signals are for. Might just be to activate some power supply or maybe a spindle brake (freno mandrino) that is mentioned in several places in the documentation.

Actually I think that PCB board where those two wires in the plastic spiral go to could be the spindle drive. So maybe the two signals are the spindle on/of and the spindle brake.