They say a picture paints a thousand words - so a schematic of what the lathe manufacturers recommend would be much easier to comment on.
To cover a few of your points - the LPT1 port on a computer has three addresses in a computer. One address is pins 2 - 9 and you are quite right - all these are outputs. Pins 1,14, 16 17 are a second set - all these pins are outputs and finally pins 10 - 13,15 are the inputs.
Pins 18 - 25 are signal return wires to the computer.
The function (input/output) of these pins cannot be changed, although with Mach3 the configuration of all the pins can be. If you have a lathe with two axis, these could well be run on pins 2,3 and 4,5 leaving the rest unattached.
The normal designation of axis on a lathe is Z axis - longtitudinal and X (cross slide).
You do not say what kind of control the spindle requires, but Mach3 puts out two types of control. One is step and direction pulses, similar to the axis motors, the other is a PWM signal (which needs to be decoded). One my machine, I have relays for "forward", "reverse" and the PWM signal to control the speed. If MaxNC uses step and direction, it is much simpler.
I do not understand why you do not think the MaxNC option will not work. I do not think you are necessarily right about pins 3,4,5. These could be outputs from the computer to the machine, not inputs. Does your paperwork not say if these are inputs or outputs.
I fail to see why MaxNC would put inputs on output only wires. Do they not intend for you to use a PC ??
Yes it is possible to use one port, but you are going to silly lengths in splitting cables. All you need is a breakout board at the end of your printer cable, which gives access to all the signal wires. You could cross patch these in any order to match up your computer with your controller. Do not buy a powered breakout board. A simple dumb board with screw terminals would do.
Don't do anything yet !!! I am quite sure the lads on the hill will be able to say whether the MaxNC mode will run your lathe. The other various "specialised" options seem to work well. No doubt someone will enlighten us.
There is probably someone who has a similar setup - give it a day or so.
Failing that I would probably plug it in and try the MaxNC mode and see what happens _ but that is up to you. You can't really do any great damage.
Yes -- Mach 3 can do threading.