any 03-05 passat b5.5 files will work and you can flash threw port. this ecu has variant coding for auto manual, reflashing the software wont change that in this one. in other cases, b5s4, early b5 1.8t, mk4 all (aside from tdi) have a auto and a manual software version but yours has both. dont use a software version from 01-02 youll end up with a bricked ecu. also if i recall correctly one of the 018dp versions from the factory are fucked up. i cant recall what version tho.
also fwiw youll wanna get yourself setup with a bootmode setup because youre playing with fire. if you brick your ecu threw the port your car will no longer run and youll be without a car. a spare ecu and knowing how to recover a bricked ecu is a must. its not a matter of when youll brick it not if. js