1. The intake manifold is identical; whoever told you that you have to keep yours is talking out of their ass: they're exactly the same. You can take yours if you feel like doing unnecessary work.
2. The mounting of the engines is the same
3. The manual transmission used in both cars is the same; automatic is different ... the housings are the same, so it will bolt up no problem, though I'm not sure how long the automatic out of a 323 would last with the extra power and torque (though I can't imagine it's life being significantly shortened by it).
4. Yes, you will need the ECU; the wiring should be identical. Keep in mind that you will have to have the new ECU re-coded by BMW to work with your car (both cars have EWS and unless you have it done, your car will not start ... normally costs around 200 dollars to have the ecu reprogrammed: I'm not sure if they need just the ECU or if it has to be attached to the car, so be ready to have the car towed if they need the car).