A HDD stores its firmware in two places. The first part is in the ROM on your PCB. The remaining parts are stored in a reserved area of the platters (System Area, SA). WDMarvel was able to retrieve all the firmware modules from the SA and the ROM. WDMarvel's ROM dump was written to flash.bin. Obviously, flash.bin is the ROM from your donor PCB whereas the SA modules are from the patient.
Using my software, I was able to regenerate your patient ROM (ROM.bin) from various SA modules. It is this regenerated ROM that you are now trying to write to your donor PCB. Clearly, flash.bin (donor) and ROM.bin (patient) will be different, as you have confirmed.
I am now trying to get you to read the same donor ROM using HDDSuperTool. If the ROM read by HDDSuperTool matches flash.bin (WDMarvel), then this will confirm that you are doing things correctly. Once we have confirmed that you have correctly reached this point, we can proceed to edit the HDDSuperTool write_ROM script and write my regenerated ROM to your donor PCB.