Also, not sure how to correct this but my speakers "pop" when I turn the radio off and on. I did connect it to pin 12 which I believe is the radio's remote on off for the amp.... Any thoughts from the "Audio Whiz Kids" out there???
I had my 2011 HD HK head unit modded by Iron Cross Audio for a low level line out (I'm assuming this is the same as the pre-amp mod you described having done). This mod was done to send a cleaner/clearer signal to my Hawg-Wired 'Six Pack' amp, for the best fidelity possible.
After checking, and rechecking my grounds, installation, etc., this pre-amp mod turned out to be the cause of my popping. I also experienced a modulating sound coming through the speakers when the rig was on, but the volume turned down (imagine if you could 'hear' your hazard lights, that's the speed/frequency of the sound).
I've since set the Hawg-Wired amp up using the stock HD HK high level out, and no more popping or extraneous sound. Didn't really notice a difference in fidelity between the two methods, either.
I discussed this problem, and solution, with both Hawg-Wired and Iron Cross, and nobody has an explanation. I should also mention that both companies bent over backward to help me find a fix, and I have no complaints with either vendor.
I'm also sure there are also plenty of people out there with this exact mod, and no issues. Maybe my Hawg-Wired amp just doesn't play well with this type of mod?
Good luck.