Lots of questions!

First off software.
For sheet work, DXF is the most common format you're likely to come across.
This will then either be loaded directly into the machine (some higher end machines will handle basic files like DXFs directly), but more commonly it'll be run through some form of CAM system to generate machine code. The most common machine code is G-Code.

I'm not that clued up on the more woodwork orientated packages, but I'm sure there is some software somewhere that will handle splitting sheets and/or creating puzzle joints.
I was going to suggest what software to do some research on, but I can't even remember the names of the more common woodworking packages :/
Fusion360 is probably worth a look at, although it has a far bigger learning curve, and the CAM side has been pretty restricted for hobby users.


Machine wise
I'm sure Jazz will be along shortly, as he has built, and I think runs his own personal vertical machine.
Any decent machine aimed at woodworking, should produce parts more accurate than you can measure.

Personally, at that size of machine, forget anything built from wood. Yes, they can work well, but unless built very well, they're not stable.
The big thing for me, is for the amount of time it would take to build a large wood machine, you could build one from aluminium/steel for a similar cost/time, and it'll be far more robust.