have you tried running an 3.5mm-to-rca cable to the amp, and then using your phone/mp3 player as a source?
it would require some software alterations to your setup temporarily, but would at least confirm that you're working with a functional amp, and the aftermarket speakers are connected properly. at this point, no audio could actually mean you've got a DOA amp.
looking over the amp manual, there's some diagnostic led's listed on page 4-- under the top cover. was part of audiocontrols back-n-forth verifying that these led's are lighting up in the correct sequence with no errors?
you could also try connecting the amp audio input from the head unit to your new door speaker wiring with no risk of damage to the speakers-- just wire nut them together. if all those connections to the amp are correct, the speakers will work, just at the lower oem power level, with no dsp control of course.
if you were anywhere near chicago, i'd be willing to take a weekend trip to look the setup over, and even bring some other gear to check other connections/test alternatives.
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