A refreshed model with Ford's "New Edge" styling themes came in 1999. Gone were many of the soft lines of the early SN-95s. Moreover, bite was added to the Mustang's bark. Even though the GT's 4.6 motor was out-sized by the 346-inch LS1 Camaros, the GT was far less expensive, and didn't have the quality issues that the F-bodies were known for, resulting in the Mustang trouncing the Camaro/Firebird in sales. In 1999, Mustang GT's power increased to 260 hp (194 kW) at 5250 rpm and a healthy 302 ft·lbf (409 N•m) of torque at 4000 rpm; redline was at 6000 rpm. Power suffered at the low end on this engine in comparison to the earlier SOHC models, but it more than made up for it at higher RPM due to the new "performance improvement" heads, cams, and intake manifold.
The 4.6 Mustang now felt more like a high winding performance motor, as compared to the earlier 4.6's, which were essentially truck motors with dual exhaust. The Mustang GT now did the 1/4 mile in just over 14 seconds, versus the 98 GT's mid-14 second performances, and in 2000, Ford very silently put in more aggressive cams and raised the compression on the GT's, as well as offering a 3.55:1 final drive. These changes put the GT solidly into the high 13's in the 1/4 mile, with trap speeds around 100 mph. Ford did leave many of their fans disappointed however, as there was a rumored(and spotted) GT with a 5.4 SOHC V8 with a 290 horsepower rating. Ford never followed through on it.
On the V6 models, split-port induction replaced single-port induction, which increased the base model's power to 190 hp (142 kW). While the Cobra claimed 320 hp (239 kW), some magazines and owners contradicted it. 5.0 Mustangs and Super Fords claimed that it actually exceeded the torque rating, but didn't quite match the power rating. There were recalls for the 1999 model year Cobras, which were given intake and exhaust improvements, putting power at 320 hp to match the original claim. As a result, the Cobra was not produced in 2000 (except the limited Cobra R) and the company developed new parts to replace the missing power. These changes were incorporated into the 2001 model year Cobra, and when fixed, these quad-cammed mustangs hurry through the 1/4 mile in the lower to mid-13 second range.
Power came from re-designed heads and cams. As a "modular" family, earlier 4.6 L SOHC's can swap out their heads with "Power Improved" heads as offered through the Ford Parts Catalog. Due to a different combustion chamber and pistons, the compression gets bumped to about 10.7:1, and requires premium fuel. The Cobras received similar improvements, as a switch was made from "B" style heads as used in the early 32 valve DOHC Modulars to "C" heads (aka Tumbleports). Redline was set at 7000 rpm for the DOHC Cobra. The Cobra also received an independent rear suspension, which was also modular.
Special Cobra R versions were available in limited editions in 1993, 1995, and 2000. Made as race cars, they were stripped of air conditioning, radios, and back seats. Unlike the early R's, one did not need a racing license to buy one of these race Cobras. The suspensions were finely tuned, and in 1995 and 2000 the Cobra R's had increased displacement engines (5.8 L and 5.4 L, respectively) that made these cars extremely potent track machines. The 1995 Cobra R used a 5.8L V-8 with GT-40 induction and a flat tappet camshaft, and was conservatively rated at 300 hp. The 2000 Cobra R utilized a modular iron block and the best cylinder head/intake system yet for the modular motors, flowing staggering numbers even in stock form. Ford tagged the motor with ratings of 385 hp (287 kW) and 385 ft·lbf (522 N•m) torque. Actual power was well over 400 hp. It received a Tremec T-56, 6-speed transmission, the same transmission used in the Chevrolet Corvette, Chevrolet Camaro, and the Dodge Viper. Minor exterior enhancements such as the addition of a front splitter and rear wing added down force and stability at speed. The Cobra used a side exiting exhaust system, utilizing actual shorty headers and three Borla mufflers. It also used "smoked" headlights, which made their way onto all Mustangs the following year.