Replacing the engine

Go through the replacement engine before you drop it in. New gaskets, seals and cleaning out things like the oil pan and rocker covers are a lot easier with the engine out. If there is any doubt about things like the water pump, timing belt, thermostat, change them. Even something like changing the head gasket just to be sure things are clean and sealed.
Yeah, it is some work but it is a lot easier with that engine out. Same with the truck side. Transmission seals, any wiring or cooling lines, new radiator hoses, heater hoses. Check over things like the brake lines, clean up any dirt/grease in the engine bay.