The 25 pin LPT1 port is actually three ports in one.
The main data port is 2,3,4,5,6,7,8,9 at address &H378. The input side of the port is pins 10,11,12,13 and 15 at address &H379 and the four secondary outputs are pins 1,14,16 and 17. Pins 18 to 25 are signal return wires. A bit of a mismash.
You should be able to use any outputs with any other, but depending how your CNC4PC breakout board is wired internally, you are better to use (as you have done) pins 2,3 - 4,5 and 6,7 as the axis outputs. Make sure, however, that each section of the board has a signal return wire connected (if required)
You will eventually require - outputs for your spindle motor, and your limit/home switches, and will soon come up against a shortage of pins. I do not bother with the charge pump - it is easier to turn the computer on, and when I have Mach up and running, then turn on the supply to the lathe electronics. Neither do I bother with the enable wires to the various axis - I can't see why you need them. If you are using the machine, they would be on anyway.
The only exception is I have an enable to my milling head because I have a combined lathe and mill - but that is a manual switch and does not use up input pins.
The way to test your outputs reliably is to go to Ports and Pins/Spindle set up and untick "disable spindle relays". Set the output for M3 to #1 and the output for M4 to #2. If you now go to Ports and Pins/Output signals then you will see you can allocate Output #1 or #2 to any pin you wish.
The M3 (#1) will output if M3 is written in the MD1 (or if the spindle start button is pressed) and #2 will output if M4 is written in the MDI line (M5 cancels both outputs) By allocating these two outputs in turn you can test each output pin on your CNC4PC board with a volt meter. I think the CNC4PC board inverts the signals, so an output may appear as a zero (when on) and 5v when off. You can reverse that by ticking active low on the Ports and Pins page.
The other thing I seem to remember is that the CNC4PC board also had different common return wires that could be wired with the various sets on inputs/outputs. This makes it difficult to set up, becasue it tries to be all things to all people.
You should, however, using the method above be able to trace the signal from the computer, along to the "input" side of the breakout board (this should be a +5 volt signal. You should then be able to trace it through the board to the output side (where it could be a 0v signal).
The inputs and outputs of all the pins are shown on the diagnostic page of Mach 3 to start you off - if it appears there it is, at least getting out of the computer.