Bottom line, the CFI 3.8 is a stinky turd.
What do you do to remedy this? The easiest way is to swap in a 5.0. However, if you are mentally deranged like myself, a Windsor V6 upgrade looks like a feasible option.
There are a multitude of later model 3.8s to throw in:
1988 Fox --- (SD - MPI)
'89-'90 MN12 (SD - ?)
'91-97' MN12 (MAF - SEFI)
'94-'98 SN95 (MAF - SEFI)
'99-'04 SN95 (MAF - SEFI)
There are many more differences between the engines and peripherals than the SD/MAF and MPI/SEFI designation, but it makes for a nice arbitrary compartmentalization.
Now that one knows where to grab a better 3.8L, the questions becomes, which 3.8L do you grab? Since the main reason for the swap is a power increase, let us sort them by power output:
1984-1987 Fox - 120 hp@3600 rpm -- 205 ft-lb@1600 rpm
------1988 Fox - 140 hp@3600 rpm --205 ft-lb@1600 rpm
1989-1995 MN12 140 hp@3800 rpm --215 ft-lb@2400 rpm
1996-1997 MN12 145 hp@4000 rpm --215 ft-lb@2750 rpm
1994-1995 SN95- 145 hp@4000 rpm --215 ft-lb@2750 rpm
1996-1998 SN95 -150 hp@4000 rpm --215 ft-lb@2750 rpm
1999-2000 SN95 - 190 hp@5250 rpm -220 ft-lb@2750 rpm
2001-2004 SN95 - 193 hp@5500 rpm -225 ft-lb@2800 rpm
1996-2003 WStar 200 hp@4900 rpm - 240 ft-lb@3600 rpm
1997-2005 Truck -200 hp@4700 rpm - 250 ft-lb@2700 rpm (4.2L)
The engine slowly gained power through the years, but the major change was the introduction of the split port intake. The split port's large power increase (>25%makes it the prime swap candidate.
The swap can be done in a multitude of ways, but the most direct is to take an entire engine, EEC and harness from a '99-04 Mustang. There are several things to be aware of though.
Clearance -
The Mustang upper should clear a stock hood.
The 4.2L upper almost certainly won't.
The Windstar upper won't either.
EEC Issues -
Even after swapping in a complete EEC-V computer and harness, there are still problems. PATS, EVAP and the returnless fuel system. All three can both be turned off with an SCT flash - problem solved.
Chassis Wiring -
I've looked through my EVTM's and can't find which wires interface with the EEC harness. However, whatever they are, a little "custom" splicing and dicing will do the trick.
Fuel Deliver -
99+ Mustangs use a returnless fuel system. The problem is that Walbro type pumps will surge and die if run with PWM. Since the 99+ Mustang pumps (vane) won't drop in, you must modify the fuel rails to keep a return system. F150 or Windstar rails are normally the ones people modify to fit.
Transmission -
You can go manual or automatic. The easiest option is to just pull the 4R70W or T5 that came with the engine.
Throttle Cable -
Unsure if Mustang cable is long enough or will interface with the pedal correctly.
A/C -
Liquid line should work. Custom hoses needed for discharge and suction
P/S -
Pressure hose might work.
Coolant Hoses -
SN95 radiator has larger inlet/outlets than Fox.
Water pump inlet and thermostat outlet are same for SN95/Fox.
Upper radiator hose is the same length for SN95/Fox, might fit...
Lower hose is 4" longer. Frankenhose may be required.
Heater core inlet hose may/may not fit
Tripminder -
Microcontroller required to convert injector pulses, duty cycle to pulse-train equivalent to DOL. Use GUFB
I'm sure I have missed several important items, but this is a draft to be built upon.
I have focused on the 3.8, but you can swap in a 4.2 (or put 4.2 internals in a 3.8) too. The 3.8/4.2 heads are the same, the main external difference is in the size of the upper intake. The truck intakes are much taller, as seen below (L-R, 01+ Mustang intake, 4.2L intake, 99-00 Mustang intake)
A few people have swapped in Windstar intakes, but those require 4" cowl hoods on SN95s. The following is a '96-'98 intake.
The Windstar intake is actually the best power-wise. It makes 7 more horsepower and 25 more ft-lb of torque than a Mustang, and the Windstar has a more restrictive exhaust. This is due to the increased height of the intake. Also, as you can tell, the intake is plastic.