This is the fun part!
You will need a helper for this. Put the engine back in the engine bay so you still need to push it forward to align the coupling to the pump. With the cab in the air, lay down on the pump and push your arm through the inside of the blower housing (this bit is really not easy or fun). You then have to try and get hold of the shaft and lift it up and get your buddy to SLOWLY push the engine forward. You don't want to pinch your fingers between the shaft and the pump!!!!! When it starts to engage, if it doesn't line up simply rotate the engine slightly to get it to line up.
Make sure you grease your universal joints before you re-install it.