The wiring harness is pretty much independent, so you just about plug s*** in if you are using the auto that came behind it. You can put a manual in back of it but i'm not read up on specifics to make it run right as neither my buddy or I decided to go that avenue. Check our Lextreme for all that nonsense.
As far as items of concern that I can think of:
-03 and up is drive by wire, so, you will need a pedal. Or, wiring harness, computer and throttle body out of 02 and down.
-you will need to buy an landcruiser oilpan (fj100), most likely directly from toyota as they are very hard to find salvage $$$
-If you use the auto it would also be wise to get a landcruiser pan for it.
-The oil filter is in an obnoxious place, use a relocator.
-i'm putting my atlas behind it, advanced makes an adapter, or I could find a junk jeep aw4 and swap tail parts and bolt it straight up. (they are essentially the same trans)
-Marlin makes an adapter to put a truck tcase behind the trans it if you want dual cases.
-If you want to run a mechanical fan, you will need one off a 2UZ, it spins backwards, no other toyota fan spins that direction that we have found.
-Physically, the engine is big, its a wide V engine with DOC, so making it fit might be challenging.
That's all I can think of, its no harder than any other swap, actually, its probably easier than a LSX swap.
pitfalls...
things to look out for.
what about all the fxxxing sensors and other things?