Is there any reason why the original radio works but when connected to a harness thats wired to a new radio, i can get the radio to turn on but nothing through the speakers.

 

It sounds like the power wires are lining up right but the speaker wires aren't. Go get the wiring harness adapter for your mustang. Then you can match the wires up to your radio from the harness. It is very easy. So, if you have already cut the wires, just put them back to your cars harness and get the adapter.