In '95 Ford built 250 Cobra R's, probably the best performing Mustang ever.  Sound proofing, A/C, the stereo and the back seat were deleted to save weight.  It came with a 351 Windsor and a firmer suspension.

'96-'97
’96 saw the introduction of the 4.6L SOHC with 215 HP in the GT and a 305 HP DOHC for the Cobra.   The original small-block that became the 5.0L had been around since 1961.   Because of tightening emissions and economy standards Ford decided it was time for a new generation of small-block engines.  The modular design makes it cost effective to create engines of different cylinder configurations--like inline 4's, V6's, even a V4, V10 or V12.

'98
Exhaust porting added 10 HP for the GT.

'99-'03
The SOHC GT and  DOHC Cobra get a significant HP increase and a slight increase in torque in 1999 via better intake, cams and larger valves.  Most of the increase is at higher RPM's.  The 3.27:1 axle is standard.  The Cobra gets an independent rear suspension.  There are moderate styling changes. Stiffer springs, smaller anti-roll bars, different shock/strut setup, and heavier steering feel is an attempt to get the same handling with a better ride. The 2000-02 carry over basically unchanged from the 1999's.

For '99 the base price of a GT was $21400, Cobra coupe $28k, Cobra convertible $32k.   2000 prices are about the same. 

In 2000 300 race-ready   street-legal Cobra R's  were released with a 5.4L DOHC, 385 HP and a 6-speed.   It comes with Recaro seats, Eibach springs, Bilstein shocks & struts, a Borla exhaust, plus many other modifications. 

Limited edition models offer a hint of the future powertrains.

For 2003 (a late 2002 model actually) the Cobra gets a supercharger with a rating of 390HP plus additional driveline and suspension changes and a 6-speed.

'04
The Mustang moves to a new platform, the S197, a shortened, modified version of the DEW98 rear-drive platform with independent suspension that's shared with the new T-Bird and the Lincoln LS.