the shaft you are referring to is the middle "driven" shaft, you can remove it without tearing the entire engine apart.
Remove the rear wheel, drive shaft and swingarm (sounds like you have done this if you can see the broken shaft with the nut on the end. Remove the 4 bolts holding the retainer and you should be able to pull the "driven" shaft out.
It always helps to buy or use a manual. Sorry, the download site has been broken for some time now and the Admin is on extended leave.
