To remove the front shaft on a 3.03 top-loader:
Remove the soft plug, about the size of a penny, from the front of the transmission case.
Go in the top and remove the recessed locking allen wrench screw that is down in the recess of the front fork. Push or lightly drive the front shifter shaft out the front. STOP> Don't drive out the shift rod. There is a detent lock and a spring under it below the shift rod. If the rod comes out the spring will push up the locking device and it is a major pain to reset it.
That's how you remove it but you don't have to remove the shift fork to remove the input shaft.
With a top-loader, To get the input (front shaft) shaft out, the shaft with the 15 small bearings, you must remove the rear bearing. That means removing the tail shaft, speedo-gear and small ball bearing that holds the speedo gear from rotating on the shaft..
With the bearing removed, the main shaft, with all the top gears can be pulled back and tipped away from the forks. This will provide enough room for the front input shaft with the synchronizers and gear to clear the front gear on the lower cluster shaft. If you can remove the front shaft bearing or slide it off somewhat it provides more tipping room.
If you wish to remove the mainshaft, gears and syncrhonizers, remove the allen locking screws from the forks. Drive out the top, rear fork, shaft. Go through the process of removing the top shaft, previously described. Tip the main shaft and the rear fork can be worked out the top and the front fork will also come out the top. Tip up the main shaft and pull everything out through the top, hence top-loader.