When it comes to LOCs I'll only recommed Dave Navone'* equipment.
When using an LOC in a factory amplified system, you need to catch the signal after the amplifier. This provides impedance matching (some factory amps like the one in the 03 Explorer I did yesterday actually shut off when it saw the LOC on its input) and a higher input voltage. The drawback to that is when the amplifier provides active equilization or crossover networks you're limited to whatever signal appears at the output of the amp. If that isn't suitible for what the system design calls for, then you're really limited to replacing the head unit.
I truely think in your case with a good amp and speaker selection (like you have), you can achieve great results using a HIGH QUALITY LOC on a factory system. I've done several vehicles including a new Acura TL with lesser quality components (RF 4-chan amp, pioneer coaxs) and was flat out impressed with the end result. Obviously you can do more with an aftermarket HU, put I'm not so quick to dismiss a quality sound system simply because it uses an OEM HU.