The reason I say the swap will be hard is because it's more than 30% increase. I know of a lot of BMW converts with a "dibatalkan" or something on their reg cards and although road legal, they can't be transferred as is to a new owner. Mine was a 328i converted to a 1JZ, so there was a decrease in capacity from 2.7L to 2.5L and my reg card is clear and transferrable. There shouldn't be any cutting on the body or subframe for a 1JZ fitment. There are plenty of aftermarket mounting kits, gearbox adapter kits and all for our kind of car. Let me know if you need clarification on anything, I've learnt through the painful way on how the car works, registered, endorsed, built and all that.
The auto diff and manual diff have different final drives. I am using an auto 328i diff now so the RPM at high speeds is a bit high for my 5speed manual but for an auto slushbox should be just nice. If you find any manual diffs let me know - I wanna swap mine out.
Stock boost for the 1JZ should be 0.3bar, very conservative. Up it to 0.8bar and you'll have a very nice to drive stock 1JZ without any serious mods.
Have you bought your engine yet?