Good morning,
Your machine could be converted into a 3 axis system, it can be time consuming if it is your first time. Do you have any of the parts for the 3rd axis? The 3rd axis kit is about $9k.
Your software version is way out of date, version 6.0 is the most current software version. You can get the software on 3.5 floppy drives or pre-installed on a Disk On Module. However you wanted to get the software onto your system, it comes with instructions. Basically plug and play.
Unfortunately, the EZ Trak does not accept G code programs.
On the EZ Trak, the home switches are the limit switches. They act in the same capacity.
I dont have any of the manuals, but I can get them from the OEM, I think they are $149.
Jon
H&W Machine Repair