Get under the truck and eyeball the crack between the engine and the transmission. I am assuming it's still not quite together and there is still a crack or gap. Carefully eyeball it, and see if it's wider at the top or at the bottom. If it's wider at the bottom, loosen the bolts you have in there already as much as you dare without them coming out. Then take a jack and jack up the transmission and wiggle it around and see if it will go.
If the crack is wider at the top, then the rear of the engine needs to come down.
Is this a manual transmission? If it is, and no matter what you do you can't get it to line up, I had one like this once, and what finally made it go, I got my wife inside to push in on the clutch pedal while I wiggled it around and it suddenly when in.