The engine crankshaft might not have a provision for the pilot bushing for the transmission input shaft, so you might be dead in the water right off the bat. Then you'd have to figure out how to get the computer to not barf when it didn't get proper signaling from the automatic transmission. One way around that might be to go with the previous generation computer, but then the instrument cluster might not work (assuming that any of the harness plugs match--chances are you'd have to make your own frankenharness), and forget passing emissions if you're in a state that checks them. For mounting, the transaxle to cradle mount from a 2AZ may work, but that depends on whether Toyota designed the 1MZ mounts to keep the bellhousing flange in the same location as the 2AZ, relative to the car, so they wouldn't need to worry about stocking different-length halfshafts. And, of course, you'd need a bunch of other parts to make it work.
You would have been better served to get a 5-speed car and try to drop in the V6. Fewer parts to change.