Mitsubishi M-TC10B Lathe with Meldas 325LG/335LG and get it going

Hello, is there anyone out there that is either still using this lathe or that used to run them that can help me figure this thing out? My company purchased this on an auction out east, we had it shipped here but it sat for some time before powering it up. Once under power it had to recharge the battery(s) as it had lost home. With the help of the books and a lot of arguments with this lathe I finally got it to home. Now here is my issue(s):

I cut and measure the diameter and the length of a bar so I have a measurement to start out with. When I went through the "pickup" part of the book I did as it explained as far as touching off, pressing the "X" to "reverse" it and the "Z" to reverse it also, I put in the diameter as measured and the length as measured into the data fields I then hit input and it gives me some funny little numbers that I am taking to mean the offset from the turret home position to the tool tip position. I then go to my Position Page so that I can establish the G54 in relation to the part and here is where I seem to lose something!!! I am not real good at using the G54, G55, G Etc. so this may be just an error in how to set up my positions, but I do what I was told and hit the "Calc" button and it takes those to funny little numbers and uses them to get my diameter and my length? But when I move back to the part with the same tol and I touch off, the position readout shows the diameter as being about .188 too big. To me it should read 2.402" but it reads 2.2.590 hence the center line is not in line with the center of the chuck at "ZERO" when I move it there? Now, I have the same issue in the "Z", it reads it to be about .275 (one of my funny little numbers) below the actual end of the part.

Another thing I noticed, when I did go through the different moves to obtain my Z zero (off by about .275) and my X zero (off by .188) i noticed that at some point the "Machine" digital numbers had changed? I thought that those numbers were "hard set" and would never change? What I mean by that is I thought no matter what, those numbers never changed from its home position? Is there a setting I don't have right on the "inside" of the computer or a parameter wrong?

Is it just that I am not seeing what the G54, G56, etc is doing?

Any help would be great...