Did you ever get this worked out? The factory-installed adapter boards for the MSD3 decoders are not the same as the 55029 retrofit adapter boards and the factory boards do not have any solder pads on them. They are effectively locked in terms of being able to add any additional capability, unfortunately. I've played around with them a lot. These factory boards also down-regulate the voltages from track power to 6.5V for the function outputs (lights, smoke units, pantographs). If you plug a factory MSD3 decoder into the 55029 the outputs will all be track power, but through the factory boards its not.
Like palmerston I'm interested in being able to control all loco functions using the MFX protocol through the decoder, so I'm wondering if there is a way to use SUSI boards and connect them to existing factory adapters. Its definitely possible with the 55029 retrofit adapter boards.