It seems like this is a bit of a mine-field.

What would be the recommended hardware to run a 3 axis milling machine with stepper motors (steppers come with their own drivers)

PC Spec and Processor/ram - laptop or desktop windows version 32 or 64 bit?
Breakoutboard?
Do some wires need to be twisted and or shielded?
Anything else?

From the NFS documentation...

Mach4 Recommended Requirements:
PREFERRED: 32 or 64-bit Laptop or Desktop – Using an External Motion Controller
Windows 10, Windows 8, Windows 7 & Windows XP with service pack 3
An appropriate external motion controller
Mach4 Plugin for the selected Motion Controller
2Ghz CPU
1GB RAM
Video Card with 256MB RAM(Large G-code files, especially 3D files will require a video card with 512MB RAM or higher)
*Use of Parallel Port for machine control only with desktop style computers with 32-bit versions of windows 7 and below.
32-bit Desktop – Parallel Port Recommended Requirements
32-bit version of Windows XP, Windows Vista, or Windows 7
Mach4 Parallel Port Legacy Plugin (cost applicable)
2Ghz CPU
1GB RAM
Non-integrated Video Card with 256MB RAM(Large G-code files, especially 3D files will require a video card with 512MB RAM or higher)


There are a number of different motion controllers to choose from (I use a Warp9 ESS and a Pokeys 57CNC - each for different applications) the only recommendation I make is "do not choose a cheap Chinese controller" - if you do then you will end up buying another just a short distance down the line.
I use shielded cable for all inputs (limit switches, etc.) and single point (star) earthing for all shields. Other than that it is just good wiring practice that is required when connecting everything.

It will be a great adventure my friend. 

Tweakie.