I'm bringing this old thread back to life to document my findings for others, who might want to replace their counter-shafts.
I used the following parts from McMaster Carr:
Rotary Shaft, P/N 1886K41, $11.26
Bronze (Oilite) Sleeve Bearing, P/N 6391K207, $2.11 each, quantity 2
Clamping Collar, P/N 6435K15, $2.20
Removing the old bearings and installing new ones was easy. I turned an aluminum mandrel to fit the bushing hole with a shoulder to catch the bushing end and gently removed the old ones out by tapping the mandrel with a rubber mallet. Then I installed the new ones the same way. Removing and installing them using an arbor press would have been safer, but I did not want to remove and rewire the motor. The McMaster bearings are virtually identical to the original Atlas bearings.
I parted the shaft at the proper length on the lathe. I milled the #3 key keyseat on the shaft and a flat for the motor pulley's set screw. I also put a chamfer on the right end of the shaft as a lead-in in case the two bearings did not exactly line up (they didn't). I used the compression clamping collar in place of the original set screw collar. The set screw collar did not stay in place well. The clamping collar holds firmly and does not damage the shaft like the set screw collar did.