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Please correct me if I'm wrong, but I think you'd at very least need to get your vin flashed to the new ecu so that the BCM is happy with the new ECU.
As far as running and driving once the security "features" are out of the way you should be fine provided it's an ecu out of a car with the same enginge/trans as you were replacing I'd imagine.
Well I was inquiring to get the motor to start, as the first responder said the car will need the pcu flashed for the car to start, then get it tuned. Thanks guys, wasn't sure if it needed flashed or not to get it to run.
Unless your current wiring harness and ECU are damaged or for some other reason not usable, you should have no problem just swapping engines. It'd also be a lot less work. Just because the engine you're getting includes that stuff doesn't mean you need to use it.