First off dont be intimidated, its really quite easy once you get your teeth into it.
Well you could do as you say and maybe the Tormach makes things simple by having plugs for everything that is outside the cabinet such as limits, index, speed control etc. If it does then you can set up your lathe to use these but I think it might be a pain to do it that way. If it doesnt use plugs for everything then it will be a major pain as you will have to wire your lathes limits, index etc to the Tormach breakout every time you want to use it and hen swap everything back when you want to use the mill.
You can use the same parallel port in the computer but if you have two distinct machines then you will have to connect the parallel port to one machine or the other. Please note this is if you are not going to try and use the same drives etc.
If you do use the Tormachs drives etc you may run into problems unless the motors are the same on mill and lathe. The drives need to be set to the current of the motors with a resistor and also there is a pot on the drives for adjusting resonance. So if the motors are not exactly the same you may hit problems and even if they are the tuning pot may need to be set different from motor to motor.
There are a few places that you can buy complete control hardware from but its more expensive that way. For a basic system you will need a power supply, breakout board, stepper motors, stepper drives and limit switches. You can easily build a power supply as they dont have to be regulated so all you need is a suitable transformer a suitable capacitor and a rectifier.
If you decide to go down the self build route you will get all the help you need from the guys on this forum.
The version Of Mach in the Tormach shouldnt really be a problem as I would think it only varies in screensets and maybe a few macros but as long as you can open MachTurn from your Tormach computer then you can set it up how you like.
Hood