3 and 6 works on all pioneer nav pieces. same buttons will do different things on ford radios all the way back to early 90's.
If you were able to view the DTC's in the nav diagnostic menu and had comm failure with the SWC then the radio after the radio was swapped it was not programmed or not programmed proerly when replaced the same goes for having no audio if it's THX. It might also be the wrong radio, either misbuilt or their radio repair center sent them the wrong radio which is pretty common. The radio compatability list almost always has error and says MKX and Edge take the same radio
if it's a 2008 MY with Sync they have to reprogram the APIM and ACM if only some of the the buttons on the steering wheel work and will show a SWC POD 2 error in the nav DTC menu
Ask your dealership to start from scratch when programming the radio, pull the "as built" Hex codes for the ACM, RSEM, SDARS, PAM modules(APIM if Sync). the VCM/IDS does not always properly take the data out of the old radio if it's defective. the only thing you will lose is your stored presets if they do it this way.
the speakers cutting out makes a difference if the MKX is equipped with THX. I honestly have only heard of this issue when the internal amplifier overheats due to to high of volume for a extended time, shorting speaker wire to ground or another speaker wire, or a shorted speaker coil. the other possiblity a plug in the vehicle (back of radio, THX amp, junction behind dash or kickpanel) might not be plugged in or inserted and locked. the nav units do have thermal protection for all of the speaker circuits, so the radio will shut down all of the audio outputs if the head unit goes into thermal mode including audio signal for subwoofer. if its THX there might be a communication fault code either in the diagnostic menu of the Nav or even if they do a network test with the VCM.
BTW cloning your DVD are a great idea of backing up, but you never need to remove the DVD unless you are updating it unless I can hack these dang things to play DVD's . I have my own personal 5P and 2008 6P that I use for testing. I have yet to find a error with my copies and I find it hard to believe Navteq would do something like that since my old Alpine DVD's were protected. both 5P and 6P ripped right to my harddrive with no problems and copy with no issues. BTW the 2007 6P gave me issues even from a new disc. I didn't bother cloning since the techs at Navteq said thay had a few bad discs go out.
if I overlooked any issues post them back up or PM me