The EZClient software used by EZ-Flash IV GameBoy Advance flash cart is really unstable so after some effort, I've managed to code a wrapper application around the EZ4Patch.dll. Also managed to figure out how the official client did the header modifications it did.
Note that this software is only intended for use with the GameBoy Advance flash cart. I haven't tested it with anything else.
Source Code: github.com/HiddenRambler/EZ4Patcher
The binaries : EZ4PatcherV1.zip