OK, I am a little confused! The 5v stereo audio mod should give you a left and right output wire - where have you connected those at the moment, presumed directly on the scart connector under the supergun? That's the way I first 'tested' my stereo audio output, but having 2 wires trailing to a supergun is a pain, and its better to replace the supergun with a DIN socket (same as AES) and output video, audio and 5v to that connector in the same way the AES is wired, but replace composite (which MVS doesnt output) with the 2nd audio channel, that way you can have an AES DIN type connector for AV which supports stereo audio. The JAMMA edge on an MV1-FZ outputs the amplified MONO sound, not stereo. The supergun might support standard stereo pinout from the JAMMA edge but as default on an MV1-FZ you would get amplified mono I think.
If you build MKL's stereo amp board and connect the 3 inputs (left, right and center) which you are already using on the 5v stereo mod board (assumed you've done what I originally did using a bunch of 4.7uF caps and a few resistors) to the 3 input points on MKL's board, feed 5v and ground to that board as well as per the diagram above (on an earlier post by someone else). Then you should be able to take the left and right outputs of MKL's board and either wire them directly to a 3.5mm socket, or under the SCART connector on the supergun, or to a DIN socket or where ever you want to feed that amplified stereo audio.
EDIT: Also, final note here - You don't need the old audio board with the 4.7uF and 4K7 resistors on it. MKL's board is designed to connect straight to the 3 (left, right, center) outputs from underneath the MVS.