You will also find the 3.9 MPFi motors have a single TPS (on the 4-speed) where the CFIs have 2 TPS plugs. This is easily gotten around by wiring the two plugs together so the box computer knows where the motor's at.
Proud TQE Operator and President of SEFAG - the Society for the Elimination of Ford Automatic Gearboxes
Pacemaker headers + 2.5" exhaust
EF Fairmont interior
Lowered King springs
5 speed manual
Newest mod: EF Ghia wiring loom and dash