Sounds like you got a 90+ wiring harness. Only the 89 is a direct plug and play. The 90 plus has a different dash harness and only has one hookup near the driver's side firewall. I believe the ford racing harness comes with only one and I believe they tell you how to rewire it. I'll dig around and see if I can find it. Here's a chart for compatibility.
1987-1988 Speed Density. All the speed density engine harnesses are interchangeable. Ford used a different computer in 86, but the engine harness is the same. The dash harness in the 86 is specific to that year car and will not work in the 87-93.
1989 Mass Air and No Air Bag. One year only harness. Only car with mass air and no air bag. The dash harness is the same from 87-89 on all models, but the engine harness is specific to the 89. The 89 harness can be used in place of the stock 87-88 harness for anyone looking to do a mass air conversion.
1990-1992.5 Mass Air with Air Bag. Fuel pump relay is under the drivers seat. The change here was made sometime in 92. All the dash harnesses for all models from 90-93 are interchangeable.
1992.5-1993 Mass Air with Air Bag. Fuel pump relay is in the engine compartment. M12071C302 is this style engine harness. All the dash harnesses for all models from 90-93 are interchangeable.
1994-1995 All the engine harnesses from the 94-95 V8 cars are interchangeable. All the dash harnesses from the 94-95 cars are interchangeable.