Special tools are needed since that long shaft is in the way.
Dennis showed how to remove the input without removing the front bearing first by dropping the cluster gear. Maybe he'll share how he removes the rear bearing.
Nothing special needed to remove the rear bearing either, but you must do a complete disassembly of the case.
Drop the counter gear and remove the input shaft as above. Next remove the shift forks, trunions, springs, and shift rails in order to remove the complete output shaft assembly out of the case. Reverse gear can remain in the case. Remove the countershaft. Then remove the C Clip that holds the bearing on the output shaft. Set the casing on end and put the whole output shaft back into place. Using a block of wood and a big hammer, hit the end of the output shaft which will drive the bearing off the shaft similar to what was done with the input shaft.
To reinstall that bearing, I put the assembled output shaft back into the case and use a 6" piece of heavy pipe as a slide hammer to drive the bearing into place. The pipe must be able to go over the output shaft and yet only contact the inner race of the bearing. After the bearing starts on the shaft, you can set he bearing partually in the case, ensuring that it is sticking out maybe 3/8" from where it normally would rest up against the C Clip that fits around the outer diameter of the bearing.
It really does work and be sure to use a little lubricating spray on the shaft and the inner race before driving the bearing on. If I have gone this far, I normally remove the needle bearings out of the countergear, clean them up and reinstall them with a grease packing then put the dummy shaft back in. The grease helps keep the needles in place and it is much, much easier later on when it is time to install the countershaft in the counter gear.