It's been a few months since I put everything in and wanted to give some updates. A few weeks after I had everything in, I noticed a slight hum during quiet portions of songs or while change stations/sources. I had a few places where my signal was close to power so I moved those, no change. I found a new ground location, no change. finally I just pulled the rcas from the audiocontrol LC2i and the buzz went away. Hooked up an ipod with 3.5 to rca adapters and it played cleanly. I hooked the RCAs back to the LC2i and then went to the signal side and found the the 12vdc and ground wires for this unit are running pretty close to the signal, I separated them and zip tied them to keep them from moving around and reduce the hum/hiss significantly. However, I couldn't completely eliminate it. I think that I might need to get power and/or ground from another source, or get ahold of some shielded wire for the input signal.
The other main thing that I've worked on is with the tuning of the system. Originally, I turned all of the dials on the audiocontrol unit down as far as they would go. Found the point where the headunit introduces distortion on several different test tones (31 was my magic number). Then set the gains on my amp. All of them ended up being set pretty close to the maximum. The sound was much better than stock but after a few months of listening to it, I realized that the system should be sounding better. I wanted it to be more cohesive and to punch a little harder.
I set everything back to zero. This time I decided to follow the instructions on the audiocontrol unit and set the main and bass levels to just below the level that would trigger the maximized lights. I then set the gain on the amps (ended at closer to halfway this time), and then set the hp filters for the doors and lp filter for the sub. Now the sound isn't just 'better than factory'. It is truly Amazing and exciting and I finally love it. Who would have figured that 'following the instructions' would have been the answer I was looking for.