Manual fixup of all branches would be rather tedious. So get a disassembler and an assembler, disassemble the file, insert your dummy command sequences, then reassemble. There's still a chance the code would break. Some executables deliberately check the integrity of their code as a copy protection measure.
If the executable was signed via Authenticode, you won't be able to restore the signature. The whole point of the digital signature is to prevent tampering of this sort.