Toader,
First, did you by any chance check the chuck or dead center runout before you took the headstock apart?
Assuming no, first think that I would do is to pull the spindle again and make certain that both bearing cups are uniformly seated in the headstock journals. If one is cocked, that would cause problems. Then I would fully seat the chuck end cone on the spindle and reinstall the spindle with nothing but the bearings and the spacer and 32T gear on the left end. Check the runout on the register behind the spindle nose threads and in the middle of the spindle and mark the high spots. Assuming that the register runout is significant (greater than 0.001"), if the high spots are both on the same side or if you have two high and two low spots, you probably have a bearing problem. If they are on opposite sides, you probably have a bent spindle. Bent spindles are common on the Craftsman AA machines. But if yours is truly bent, it will be the first case I ever heard of on a 10" Atlas.
On an unrelated subject, several posts down this thread, I wrote briefly about the 1955 and earlier Atlas Manual of Lathe Operation. Since then, I've acquired copies of what, after a year and a half of looking, I'm moderately confident are all of the only 6 actual versions up through 1955. The first four all have only 1937 on the copyright page (back of the title page).
The first version (I have two examples from different sources, one a repro and one a PDF) has a complete Chapter 7 (Threading) and covers the Atlas 10D and earlier. If you ignore the lack of tumbler gears on the threading chart, it would also cover the Craftsman 101.07400. 101.07401 and equivalent babbit bearing models. These are all of the 10" and 12" that shipped with two 96T Change Gears. All of the photos in the manual are of 10D or earlier. The 6" is not mentioned.
The second has no pages bound into Chapter 7 but originally shipped with one of the other of two separate Threading supplements. One covered the Atlas 10F and the other covered the Sears Master Craftsman 12" 101.07402, 101.07403 and equivalent babbit bearing models. Outside of the supplement, most photos were changed to the 10F. I have seen recent evidence that this version was still being sold at least as late as July 1943.
The third and fourth are the same as the second except that the supplements are bound in and the binding changed from wire to plastic. Both say Atlas on the front cover and neither mention the 6".
The fifth and sixth are the 16th edition of 1955. One still has a black cover but says Craftsman on it instead of Atlas. The other has a gray cover and says Atlas. Chapter 7 covers either Craftsman 12" and 6" or Atlas 10" and 6" respectively, plus the appropriate QCGB models. And these two versions are the first to show print history on the copyright page. The number of reprint years shown is 17, not 15. So I'm not sure how they came up with "16th Edition".
Robert D.
Robert D.