I am assisting my son with a stereo his replacement. His current system is factory Ford system with 6 disc changer in trunk, amp under driver seat and am/fm cassette in dash. We have new faceplate and proceeded to replace. The wiring harness shown in this forum does not match either the existing unit or the connections at the amp for the speakers. The power wiring is alright. Can anyone give some insight on the best way to wire for speakers? I can run wire from the head unit to under the seat if needed or could he use that amp?

The metra installation kit includes the appropriate wiring harness to allow you to use the amp.
Metra 99-5720
We purchased the scosche kit for his car but the speaker plug is not correct. The one we recieved is similiar to the power plug (different wire colors) but similiar arrangement. His has several more wires than what was recieved. Plus the colors in the database here does not match what we have.
Actually, the plug recieved looks like other kits I have seen. I willtry to upload a photo of what we have.
We got everything going. Here is what we had in case others need info.
The kit we ordered came with proper plugs. 1 for power connections, anothrr for speakers. The speaker plug connection was hidden. Once we found it, it was set up as a loop connection from existing amp located under driver seat. This connection was an output to the front speakers. This allowed us to use the existing wiring from new plug to old amp to connect to rear speakers. Once we located the correct wires, we used some copper wire to create jumprs to "bridge" this connection for rear speakers.
This took a little time verifying proper wires but turned out to be good arrangement.