Here's my list, hope it helps.
To reference the machine, jog z in the negative direction (down), and jog y in the negative direction (towards the column). Type in the R key for reference, and jog the z axis in the positive direction, it hit the reference switch and come to a stop. Do the same for the y axis, and the x axis. This should reference all three axis. You also need to see where the home position is located for this machine. Go to Mode Select S, for set up, on one of the screens you will see the home position coordinates. I usually set these depending on the machine travel limits. For example I have two J-425 machines with x travel of 30" and y travel of 15". I set my home positions at x15.000 and y15.000. So after you reference the machine send it home by pressing Mode Select 0, then H, and jog the x axis and the machine will travel from the reference postion to the home position. I usually zero out the axis at this point.
The machine did have the option of digitizing with a probe, you could upgrade this machine to a Delta2000 control and get this option. Give the control a chance, it's not too archaic, it's really pretty powerful, being able to mill a pocket with two lines of code, whereas a Fanuc would require many more.
The jog controls should work, I have an opposite problem on one of my machines, the jog controls work but the handwheel doesn't. Call a tech out on that one.
You can connect to a PC via RS-232, I have all of mine connected this way.
I don't know of anyway to download a manual, I could possibly help you out with that, PM me.
These machines are what I cut my CNC teeth on, let me know if I can help in any other way.