Use tmpgenc or wombles and de multiplex the mpeg.
You will have to encode your new audio stream to make it compatible with your original mpeg.(depending on if it was a vcd or svcd or other).
You can do this with tmpgenc, although it will probably take an hour or so and then multiplex the files back together.
You will also probably get audio sync problems.
There is a Chickenman tutorial to help solve these.
Good luck!