Just wondering. What model year Mustang are we dealing with? 1996-1998 (coil pack) or 1999-2004 (COP)?
Since you stated "spark plug wires" I'm going to assume this is a coil pack ignition system.
Confirm HOW you are testing for spark. With an external spark tester?
Are you absolutely positive that the correct plug wiring has been used? The correct cylinder to coil pack tower? The coil pack ignition is affected by spark plug wiring routing.
What have you done to rule out a problem with the signal return lines to the PCM? Have you tested for opens or short to ground?