You can download the software for the Prolight 2000 with ATC on the web. I also have it and can zip and email it to you- it's a free download since these machines are no longer supported. You only need one computer to run the machine- and you do not need one of the control boxes- everything needed to make the machine go is in the "backpack". The computer should run a true DOS base- such as Win98 or Win95 or plain ol' DOS. The DOS emulation in Win2K and XP will not do the job. I use Win98 and it is great.
We're just getting familiar with one of these machines as well- it's been sitting around for a bit but that is soon to change. No tool changer- so I can't help you with that. This is the first time I have experienced a servo system- the silence while the thing moves still freaks me out- not to mention the speed compared to my stepper systems.
I'm not in the shop right now so I can't look- but I think there is only one serial cable to connect the mill to the PC. I also have a cable running from the 4th axis to the underside of the backpack. However, I have an older version of the 2000 with the power switch on the back- the later models had the power switch on the front and a lot of stuff going on in the back that I am not familiar with- although setup of hardware is covered in the PLM2000 user manuals I think.