My Dad put an engine and transmission in a 1996 Explorer. When you buy a crate engine, you're getting a long block - not all the little things, that are required for the thing to actually run.
You have to transplant an assload of sensors and what not from the existing vehicle, onto the new engine.
Since replacing the engine and transmission (and he did this himself - he could never afford to have a shop do it), he's:
Replaced the fuel injectors, IAC motor, rebuilt the rear diff, shocks, speed sensors, fixed a million electrical gremlins (interior shit), radiator, body mounts, alternator, brake master cylinder, power steering pump, steering rack, heater core, ECM, EGR valve, u-joints, had the transfer case rebuilt...and a bunch of other shit I know I'm forgetting. All this, over the course of about 3 years.
And at the end of the day, the thing is worth maybe $2,000. Maybe.
Buy the best HondaYota for $5k you can find.