Jesse, I'm wondering why you need the FAI-3?
We normally use it to take speaker level outputs from an aftermarket HU, and force them down to match the M&T amp.
If you're not using the M&T amp, but are using the stock stereo with an aftermarket AMP, then that would also work out for you to create the RCA inputs the aftermarket unit needs.
In all cases, you may need to adjust the gain with the lil adjusters.
Keep in mind, you need something to turn on the remote amp in all cases, and on the METRA harnesses, its the blue/white wire.
Your last paragraph leads me to think you are not turning the aftermarket amp on with the blue/white wire.. etc.
I have a JVC HU, and have the FAI-3 to convert down to the level the M&T amp wants.
You may want to read all the other stickies in the audio section since there are things mentioned like:
Do you have M&T or not? (M&T uses 2 ohm speakers)
Proper wiring to the M&T amp vs aftermarket.
Hope this helps..