It's much easier to mate the engine and tranny outside the vehicle. Then install using a cherry picker from the side, not the front. Most cherry pickers don't have enough reach to install from the front. Take off a front wheel, block the suspension, and install from the side. Be sure to have someone in charge of sticking the driveshaft in the tail snout as it all goes in. Ask me how I know that...
My headers have individual primary pipes and could be installed after the engine is in.