The two power saving signals are also accessible on the board as PFM and PSF, you can brigde them with a piece of wire to 5V to disable one or both of the 2 modules. They have pull-down resistances, so if they are not actively driven/bridged, they will default to enable both modules.
If you use the parallel method, it works principally, but the two ports fight over the right to communicate with the USB, therefore sometimes if both are enabled the PC might recognize one but not the other (obviously they cannot be used at the same time over the same USB port). In the FX-SaberOS code I included 2 config modes,one for programming which disables the MP3 chipset and the audio amp and one for sound file upload, which disables the FTDI.
But very honestly I have my doubts if the code really disables the right module. So please check, it's for sure A2 and A3, but which controls which I'm not so sure about. I need to test it out still.