Hi Elmo,
It sounds like you have an interesting project
The model number you quoted is for a 12" lathe when I did a quick google.
Yet you say your lathe is only 4 1/2 inches from the center of the spindle to the bed.
On a 12" lathe this should be 6". This 12" measurement is other wise referred to as the swing.
6" Center Height = 12" Swing.
I have a 10" swing model and my center height is exactly 5" from the long flat bed way.
I use this measurement to set my tools at center height.
From what I understand Craftsman was just Atlas re-badged.
Other people here may have more ideas why you are seeing this difference in the size.
Did they make a 9" Craftsman ?
You should still be able to find most of the parts you need.
I managed to replace the half nuts on my lead screw but as you would expect they usually aren't cheap.
Good luck and keep us posted with your restore.
David