Audi A4 Reflash

Hi there. Original vehicle, Audi A4 B7 model, 2008, 2.0 ALT engine, no turbo. I removed the engine and replacing it with a built 1.8T AVJ engine with a turbo upgrade. I also made the "wise" decision to do a engine bay shave.........-_-. Anyway, I am going to rewire the car (using the practical club motorsport rewiring course). My question is, can I reflash and use the factory ECU ie, is it sufficient to do the job? If so, what is the support like to do the re-flashing.

Otherwise, when you do a custom rewire, must it go into a standalone ECU?

Thank you in advance.