Im doing a hz diesel conversion on a friends truck and needed to install a 1hz input shaft into his new h55 transmission. I have the service manual which shows how to disassemble the trans but I was pretty certain all the steps were not necessary to swap the input shaft. So here is what I did. I didn't intend on doing this write up until after I was done so in hindsight I could have taken better pictures of the steps. Following these steps and having the service manual handy should make this a one banana job. 
Im starting with a brand new transmission from Toyota so im going to omit the removal of the transfer case since the new transmission doesn't come with one.
In a nut shell one only has to remove the top cover, fifth gear assembly and extension housing (this is the gear on the back of the trans), and both counter shaft (lower shaft) bearings so the shaft can drop down enough for the input shaft gear to clear the countershaft for removal.
Start off with removing the reverse light switch on the front side of the top cover. The manual says a special tool is required for this but I simply used a 28mm wrench. (the switch is 27mm but I didn't have that size handy at the time) The 28mm wrench worked well because it was large enough to clear the wires for the switch but still grab the switch body for removal. Someone had borrowed my 27 so I had to make do. Next make sure the trans is in neutral and remove the 14mm bolts holding on the top cover and remove the top cover. The fifth gear selector and boot will come apart if you turn the cover just right while removing so unscrewing the retaining bolt for it is not necessary.
Next remove the 6mm allen plug on the right side of the trans and using a magnet remove the spring and detent ball behind the plug. This is the fifth gear selector detent. Once this is off the extension housing can be removed from the back of the trans.
Next remove the 36mm nut on the back side of the counter shaft and using a puller remove the fifth gear assembly as a whole. On the very front side of the fifth gear there is a spacer and small dowel that will probably fall out when the gear slides off but no worries as it simply goes back in the counter shaft when everything goes back together. Also be careful with the two needle bearing halves that the fifth gear rides on. The shift fork and shaft it slides on can now also be removed. (note for reinstallation) (the rear most gear is what is holding the fifth gear assembly on the counter shaft so even though its removed as a whole it will be reinstalled separately from front to back and only that rear most gear will need to be pressed on)
Once that is out of the way remove the four 12mm bolts holding the rear bearing retainer and remove the retainer. This retainer holds the counter and output shaft bearing so even though the output shaft is staying in the trans it must be removed to remove the counter shaft bearing. Remove the retaining ring and using a puller remove the countershaft rear bearing.
Next up remove the seven 12mm bolts holding the front bearing retainer on and remove the bearing retainer. Remove the two retaining rings on the front of the counter shaft bearing and using a puller remove the bearing. The countershaft will drop down once this bearing is removed.
Now remove the two retaining rings on the input shaft and remove the front input shaft as a whole. I used a small pry bar against the trans case and the retaining ring land to gently remove the shaft prying on one side then the other until it came out. The big bearing will stay on the shaft at this time. Once the bearing is close to clearing the case take note of the needle bearings on the rear part of the input shaft. I was lucky and mine still had assembly grease on them so they somewhat stayed in place.
I used a puller to remove the bearing from the old input shaft. I reinstalled it on the new shaft using a block of wood and piece of capped pipe (or actually an old jack stand). (I wrapped the new shaft with saran wrap then duct tape so that it wouldn't get scuffed up inside the jack stand...errr special tool) Once the bearing is on, the small retaining ring can go on the shaft and the larger one can go back on the bearing. I found it easy to at this time install those needle bearings into the new input shaft. Mine still had a good bit of assembly grease on them so they stayed put pretty well but, when you put the last one in they actually kind of snap in place and stay put. At this point the input shaft is set back in place using a plastic hammer. It is driven in until the retaining ring contacts the case.
Install the retaining rings back onto the counter shaft bearings and loosely install both bearings so as to mesh the gears of the input shaft. Then one by one, drive in the bearings with a plastic hammer until the retaining rings contact the case. Install the rear bearing retainer and torque to 13ft lbs. Install the dowel pin and spacer onto the back of the counter shaft and then slide on the fifth gear assembly and shift fork. Again these parts simply slide on and only the rear most gear will need to be pressed or hammered on. I used a 45mm socket to do the hammering so as not to damage the gear. While your hammering the gear back on it is a good idea to place something against the front of the counter shaft to keep it from sliding forward. Once the gear is back on reinstall the 36mm stake nut and torque to 94 ft lbs.
Reinstall the front bearing retainer and coat the bolt threads with your favorite gasket compound so you don't have any leaks and torque to 13ft lbs. Reinstall the extension housing, detent, spring and hex plug and finally the top cover.
Im starting with a brand new transmission from Toyota so im going to omit the removal of the transfer case since the new transmission doesn't come with one.
In a nut shell one only has to remove the top cover, fifth gear assembly and extension housing (this is the gear on the back of the trans), and both counter shaft (lower shaft) bearings so the shaft can drop down enough for the input shaft gear to clear the countershaft for removal.
Start off with removing the reverse light switch on the front side of the top cover. The manual says a special tool is required for this but I simply used a 28mm wrench. (the switch is 27mm but I didn't have that size handy at the time) The 28mm wrench worked well because it was large enough to clear the wires for the switch but still grab the switch body for removal. Someone had borrowed my 27 so I had to make do. Next make sure the trans is in neutral and remove the 14mm bolts holding on the top cover and remove the top cover. The fifth gear selector and boot will come apart if you turn the cover just right while removing so unscrewing the retaining bolt for it is not necessary.
Next remove the 6mm allen plug on the right side of the trans and using a magnet remove the spring and detent ball behind the plug. This is the fifth gear selector detent. Once this is off the extension housing can be removed from the back of the trans.
Next remove the 36mm nut on the back side of the counter shaft and using a puller remove the fifth gear assembly as a whole. On the very front side of the fifth gear there is a spacer and small dowel that will probably fall out when the gear slides off but no worries as it simply goes back in the counter shaft when everything goes back together. Also be careful with the two needle bearing halves that the fifth gear rides on. The shift fork and shaft it slides on can now also be removed. (note for reinstallation) (the rear most gear is what is holding the fifth gear assembly on the counter shaft so even though its removed as a whole it will be reinstalled separately from front to back and only that rear most gear will need to be pressed on)
Once that is out of the way remove the four 12mm bolts holding the rear bearing retainer and remove the retainer. This retainer holds the counter and output shaft bearing so even though the output shaft is staying in the trans it must be removed to remove the counter shaft bearing. Remove the retaining ring and using a puller remove the countershaft rear bearing.
Next up remove the seven 12mm bolts holding the front bearing retainer on and remove the bearing retainer. Remove the two retaining rings on the front of the counter shaft bearing and using a puller remove the bearing. The countershaft will drop down once this bearing is removed.
Now remove the two retaining rings on the input shaft and remove the front input shaft as a whole. I used a small pry bar against the trans case and the retaining ring land to gently remove the shaft prying on one side then the other until it came out. The big bearing will stay on the shaft at this time. Once the bearing is close to clearing the case take note of the needle bearings on the rear part of the input shaft. I was lucky and mine still had assembly grease on them so they somewhat stayed in place.
I used a puller to remove the bearing from the old input shaft. I reinstalled it on the new shaft using a block of wood and piece of capped pipe (or actually an old jack stand). (I wrapped the new shaft with saran wrap then duct tape so that it wouldn't get scuffed up inside the jack stand...errr special tool) Once the bearing is on, the small retaining ring can go on the shaft and the larger one can go back on the bearing. I found it easy to at this time install those needle bearings into the new input shaft. Mine still had a good bit of assembly grease on them so they stayed put pretty well but, when you put the last one in they actually kind of snap in place and stay put. At this point the input shaft is set back in place using a plastic hammer. It is driven in until the retaining ring contacts the case.
Install the retaining rings back onto the counter shaft bearings and loosely install both bearings so as to mesh the gears of the input shaft. Then one by one, drive in the bearings with a plastic hammer until the retaining rings contact the case. Install the rear bearing retainer and torque to 13ft lbs. Install the dowel pin and spacer onto the back of the counter shaft and then slide on the fifth gear assembly and shift fork. Again these parts simply slide on and only the rear most gear will need to be pressed or hammered on. I used a 45mm socket to do the hammering so as not to damage the gear. While your hammering the gear back on it is a good idea to place something against the front of the counter shaft to keep it from sliding forward. Once the gear is back on reinstall the 36mm stake nut and torque to 94 ft lbs.
Reinstall the front bearing retainer and coat the bolt threads with your favorite gasket compound so you don't have any leaks and torque to 13ft lbs. Reinstall the extension housing, detent, spring and hex plug and finally the top cover.
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