The factory alpine wireing harness will work with any aftermarket alpine, although this is just for power/ground/remote on.
There is a large mulit-pin cable that sends signal to the amp in the back of the car which drives the speakers.
I just re-did the whole thing. The back of the amp that is in the trunk has a diagram of what cable is which.
I bought an 4 channel alpine V-drive amp with cross over that fits into the factory location with no modification. I ran 2 sets of RCA cables to the amp from the output on the head unit. The factory power/remote on/ground that was used on the factory amp (in the back) can be used on the aftermarket amp. Same is true with the speaker wires that go to the factory amp. I spliced them and ran them to the new amp. I ditched the useless rear speakers in lieu of a sub.
I think pretty much all alpine dealers carry the V drive series. I think the amp was like $230 and the head was about $250 the eclipse speakers were $199. I removed the rear factory speakers alltogether. They are useless. But the amp I have fits perfectly and has a built in sub woofer crossover and mid/high crossover. The new head unit has subwoofer output so you can tweek the crossover frequency there too.
How does it compare to stock? Like am radio to Compact disks.
Head is ALPINE CDE7858
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Amp is MRP-F200
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Hope that helps.