If this is like other machines, there are two bearings near the bottom of the spindle separated by two spacers.
The spacers should be the same thickness, and there should be a nut putting pressure on the center of the top bearing. (the bearings should be in 'DB' configuration. (Back to Back) If you had them off, you should be able to hold the center races together, turn the outer race and both outer races should turn.
Now, the 1st troubleshooting question I have - did you have the base holding your indicator on the spindle housing, or on the table? You may have a loose gib that may only need a little adjustment. What you are interested in finding for certain is what is actually moving. You can get a little deflection in a tool if you are far enough from the spindle nose.