The factory service manual says to press out the countershaft using a hydraulic press. I accomplished the same thing using a brass drift and a small sledge hammer. Do not use the hammer by itself, you WILL damage the countershaft and you run the risk of cracking the case if you miss... You can see the progress at the other end as the other bearing slides out. Be careful as the bearings leave the casting, do not damage the gear as it enters the race. Using the bearing puller again, remove the bearing without damaging the gear behind it. You can then pull the countershaft up and out of the lower case. Then remove the remaining bearing with the bearing puller and then reverse what you just did. Install new bearings and reassemble the countershaft and reinstall it in the lower case. Set the whole assembly aside and turn your attention to the main shaft again.