Your 1990 GT has a width of 68.30.
The 1994 GT has a width of 71.80.
It's possible that the reason it sticks out is because the parts your using are from a wider car than yours.
1995 Mustang GT 5.0
BBK CAI, Pro-M 75mm MAF, Pro-M Optimizer, BBK 70mm TB, GT-40 Intake, 24# Injectors, AFR 165's, 1.7 Roller rockers, Crane 2040 cam (E-303) BBK Equal Length headers, BBK O/R X-pipe, Flowmaster American Thunder 2 Chambers. FMS 3.73 Gears, Lentech AODE 2800 stall, BBK 255lph Fuel Pump, BBK Fuel Pressure Regulator. MSD 6AL, Steeda UDP's, FMS Aluminum drive shaft, Autologic chip Larocca tune.