First off need more info on the speakers you want to use...

The factory amp includes the crossovers, EQ, speed sensitive EQ, limiters, and delay. it is a 6 channel amplifier designed to run at 2 ohms. Two channels (full range + highpass on the low end) run the doors, 4 channels are used to run the pair of dual coil woofers behind the seats with a low pass filter.

1. If your speaker of choice is 4 ohms you are going to loose half the power of the amp
2. The EQ is set for the speakers that are in the car so don't be surprised if the new speakers don't sound as good as you thought they would.
3. Wath the size of the magnet on the door speakers and check the tweeter mounting as the tweeter from the factory is situated in a waveguide.