3 speed transmission question

[cknfrmr]

I am pulling the 3 speed transmission out of my 69 C10 and came across a sight that made people think I was out of my mind until they saw it for themselves. On the transmission where it bolts up to bell housing the top two bolts I am able to take out but the bottom two I can not due to the fact that they are thread with no heads on them. What is the reason for this? Is the only way to get the transmission out to pull the whole motor? Was going to try and put a new clutch in while tried to pull trans mission. I tried to unbolt the 4 bolts on the back half of the transmission with a friend helping me and cant get the back half of transmission off either. Does anyone know what I did to screw that up? I am a ROOKIE at this. Thanks in advance for any help you can throw my way. Trying to learn with hands on and not break anything.