I will try my best to be some assistance....
I'll start by saying, stop reading if your car has fiber optic. I don't know much about fiber optic.
Now that thats out of the way.....
You have 2 options to your mod.
Option 1
Remove entire system to include DSP and amp. This is highly recommended due to the fact of less splicing and research in schematics. You can get a small 100-200watt 4ch amp and be satisfied. All that is needed is a basic wire harness for your new head unit. You will then run new RCA patch cables from the head unit to the amp and then connect the amp to the speaker cables (where the oem amp was).
Option 2
If you wish to utilize the DSP and oem amp, you will have to research for the schematic to the DSP. Your radios' RCA line OUTPUT will need to be connected to the DSP to provide it with signal. The DSP then sends the signal to your amp in the trunck. Make sure you get a radio with these outputs. DO NOT USE THE RADIOS' SPEAKER LINE OUTPUTS, for this will distroy your DSP and amp.
As for the radio, its up to you what you like, but an IPOD direct connection is better for sound and to control thru the radios control. An AUX input is more versitale (ANY MP3,CELL PHONE,LAPTOP,ECT) can be connected to it. However sound quality is so-so.
There is more than 1 way to skin a cat......remember that.