well without any specific information, it seems your processor isn't getting correct inputs (assuming all the hardware and sensors are ok). So basically, you'll need the correct harness for your vehicle.....not a whole lot you can do unless you want to rewire most of the engine sensors, in which case you may want to get a Ford EVTM (Electrical and Vacuum troubleshooting manual), and shop manual, and PCED (Powertrain Control and Emissions Diagnostic manual). This would cost alot of money......which would be better spent on the correct harness.
By the way, why did you replace your harness and what did you replace it with.
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem 
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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