TDog,
If you haven't already done it, go to DOWNLOADS (instructions for navigating DOWNLOADS are in the Sticky area at the top of this Forum) and download Atlas Mill Bulletin MMB-5 M1--MHC Rev6.pdf.
To add to what was written earlier, in the right side of the large spindle gear (AKA Bull Gear) is the Direct Drive Pin. When the machine is in Direct Drive, the pin is pushed in so that the hidden end of it enters a hole in the right or front face of the pulley, locking the two together. Locate that pin and make a mark on the pulley with a Magic Marker in line with the pin for future reference.
After you have re-positioned the spindle components, pull the pin out so that the pulley is free to rotate independently of the Bull Gear. There is a special tool for that purpose. The factory drawing for the tool is in DOWNLOADS.
Remove the oil plug (there is only one in the pulley, not two, and it looks like a set screw) from the pulley and squirt some SAE 20 (ISO 68) Non Detergent oil into the hole(it probably hasn't been done in years). Reinstall the plug and briefly run the motor to distribute the oil. Repeat at least once this time only. In the future, if the back gears are used routinely, oil the pulley bushings before each use. Otherwise, oil them about semi-annually. The rest of the instructions above are correct except that the running clearance between the pulley and the bull gear should be about 0.002" to 0.004".