I recommend pulling the engine by itself. I have done a 1MZFE swap in a Sienna with only the engine pulled. If you can do that, you can do pretty much any Toyota engine.
In short do the following (doesn't have to specifically be in this order):
1. Jack up the vehicle and support it on jack stands.
2. Remove the hood
3. Drain the radiator coolant.
4. Place a jack under the differential to keep the transmission fairly level remove the intake piping.
5. Remove the radiator hoses from the engine and transmission (if automatic), disconnect fan and sensor wiring, and remove the radiator assembly.
6. Disconnect the fuel rail feed line from the fuel filter.
7. Unplug the ECU and remove all wiring not attached to the engine (transmission, fuse box, grounds, etc.)
8. Remove the exhaust pipe from the manifold.
9. Remove the drive belts from the engine.
10. Unplug the A/C compressor clutch connector, unbolt the A/C compressor from the engine, and hang it out of the way (bungee cord or something).
11. Unplug the power steering pump pressure sensor, unbolt the power steering pump from the engine, and hang it out of the way.
12. Remove all MAP sensor hoses, brake booster hoses, and other loose wiring or connections from the engine to the anywhere else on the car.
13. If automatic, remove all of the torque converter bolts from the engine.
14. Support the engine with a hoist.
15. Remove all of the ENGINE mounts (passenger side axle must be removed for rear bracket).
16. Remove all of the bellhousing bolts.
17. Verify nothing is holding the engine to the car (hoses, wiring, fuel lines, etc.).
18. Remove the engine from the car WITH the wiring harness attached to the engine.
19. Swap over harness and better parts to your new engine (sensors, etc.). This would be a good time to relocate the EGR VSV to the intake manifold.
20. Installation is the reverse of removal.
Hope that helps.