Re: Vehicle Anti-theft system by-pass
Not a Mazda guy, but ...
The Body Control Module is what causes the headlights to come on most cars.
It also does power windows, instruments, interior functions, wipers, etc.
Since you already got rid of the ECM, this might be problematic, if it's in charge of communicating via the OBDII port. You won't be able to reflash via the port.
You really need to ask the question at a Mazda performance forum, where folk do engine swaps. On GM's, we program that feature out of the computer. I imagine the same is true for other brands.
Somebody might be able to reflash your BCM if you send it to them.