Here are many of the differences, taken from an article on the 2001 Z06 when it first debuted. Check the links at the bottom for the many changes for the 2002-2004 Z06's....
The aluminum block casting on the LS6 deletes machined holes in the LS1 bulkhead and adds cast-in "windows" that allow better bay-to-bay breathing. On the downstroke, the pistons push air back toward the crankcase, creating backpressure or resistance, and that translates into parasitic horsepower loss because it resists piston motion. With the overtravel windows, air is allowed to move more freely between crankcase bays, thus relieving the unwanted pressure.
LS6 pistons are cast from high-strength M142 aluminum alloy and reshaped with a slightly different profile than those in the LS1. In side view, the LS6 pistons have a slight barrel shape, almost imperceptible to the naked eye. The new alloy increases engine durability at racetrack operating levels, while the shape reduces internal mechanical noise.
The LS6's aluminum cylinder heads are cast with pent-roof combustion chambers that are smaller than the LS1's. Compression ratio increases from 10.1:1 to 10.5:1, improving thermal efficiency and increasing horsepower. Intake and exhaust ports in the LS6 head are refined and more precisely cast, contributing to the engine's overall increase in volumetric efficiency.
The LS6-specific, steel-billet camshaft contributes more than any other single piece of hardware to the LS6's horsepower gain. In simple terms, the cam opens the valves quicker and allows more air to flow into the combustion chambers. Cam lift increases from the LS1's 12.7mm to 13.3mm.
Stronger Valve Springs
To accommodate valve operation with the high lift/long duration cam, the LS6's valve springs are stiffer and sturdier. They are made from the same steel wire as those in the LS1 but are wound tighter for a higher spring rate.
Additional air flowing into the LS6 heads would serve no purpose without an equivalent increase in the amount of fuel to take advantage of it. New injectors increase maximum fuel delivery from the LS1's 3.3 grams per second to 3.6 grams per seconds, for a 10 percent improvement.
Internal PCV System
The LS6's application in the Corvette Z06 creates additional demands on the crankcase ventilation system. The Z06 is capable of cornering at more than 1 lateral g, requiring a special high-performance ventilation system. To prepare the Z06 for all-out driving, the LS6's PCV system is moved into the engine's V, or valley. The unique aluminum valley cover incorporates composite oil-separating baffles and PCV plumbing. All of this reduces oil consumption during high-performance driving and, as an added benefit, also reduces the amount of external plumbing, eliminating potential oil-leak sources.
Thin-wall cast-iron exhaust manifolds replace the previous stainless steel manifolds to improve durability, given the LS6 engine's potential for being involved in sustained high-speed driving.
To further maximize the breathing capabilities of the LS6 and significantly reduce vehicle mass, a new titanium exhaust system was developed for the Z06. This marks the first-ever use of titanium in the exhaust system of a mass-production vehicle. The titanium portion of the Z06's exhaust system starts just forward of the rear axle, then goes over the top of the axle to the muffler. The entire muffler, all of its internal parts and exterior skin, the outlet pipes, including the exhaust tips, are constructed of titanium. The Z06 muffler is a completely new design featuring larger-diameter louver tubes inside the mufflers to reduce backpressure and provide less restriction for the exhaust gases flowing through the system. The exhaust tips are different too, with four 3.5-in.-dia. tips to visually set the Z06 apart from the standard Corvette. Titanium offers a lower density than steel, and higher strength than either magnesium or aluminum at all temperatures. It reduces the Z06's weight by 17.6 pounds a whopping 50 percent reduction compared to the weight of the stainless steel exhaust system used on the Corvette coupe and convertible. In addition to easing exhaust gas restrictions, reducing mass and looking distinctive, this exhaust system sounds more aggressive than that of the standard Corvette. Considerable time and effort went into the design and tuning of the mufflers to ensure an exhaust note that would be unique to the Z06.
In addition to providing more power and better fuel economy, Corvette engineers upgraded the operation and durability of the rest of the Corvette powertrain.
The driveshaft is upgraded from a metalmatrix composite to aluminum alloy 6061, and it is increased in diameter from 55mm to 63mm. Driveshaft couplings have also been upgraded on manual-equipped models for additional strength and durability.
M12 6-Speed Manual
This transmission is unique to the Z06, and is the only transmission available for that model. It is not available on Corvette coupes or convertibles. It has more aggressive gearing to increase torque multiplication in most forward gears, allowing for more rapid acceleration and more usable torque at higher speeds. A transmission temperature sensor was added to protect the M12 from higher thermal stresses. The sensor warns the driver via the Driver Information Center with a TRANS OVER TEMP light if thermal loads become excessive, meaning that the transmission could be damaged if not allowed to cool down.
1st Gear 2.66:1 2.97:1
2d Gear 1.78:1 2.07:1
3d Gear 1.30:1 1.43:1
4th Gear 1.00:1 1.00:1
5th Gear 0.74:1 0.84:1
6th Gear 0.50:1 0.56:1
Reverse 2.90:1 3.28:1
Carbon blocker rings have been installed on all manual transmission forward gears to provide for smoother shifts and additional robustness.
The Z06 features a suspension system all its own designated FE4. It's not available on other Corvette models but is standard equipment on the Z06. It features a larger front stabilizer bar, a stiffer rear leaf spring, revised camber settings and unique shock calibrations, all engineered with a bias toward maximum control during high-speed operation. The suspension component specifications are: Front stabilizer bar diameter (hollow): 30mm with 4.5mm-thick walls. Rear transverse composite spring leaf: 125 N/mm versus 113 N/mm of the Z51. Camber, front and rear: Z06: -0.75° (coupe/convertible: -0.25°). The Z06's negative camber helps to keep the tire flatter in relation to the road, and raises the tire contact patch for greater grip while cornering. When coupled with other special Z06 components, the combination provides unparalleled, all-out racetrack performance, which is what the Z06 is all about. During development testing, Corvette engineers were able to generate racetrack speeds that improved Z06 performance by an average of 3 to 4 seconds per lap over last year's hardtop model on typical 2-mile closed-circuit road courses. This we were able to test for ourselves at the Mid-Ohio Sports Car Course in Lexington, where we had the chance to drive a standard coupe and a Z06, back to back.
Z06 wheels are wider front and rear than those on the standard Corvette: The new wheels are also one of the visual identifiers for the Z06, letting onlookers know that this car is something special. They are uniquely styled, and are the most mass-efficient aluminum wheels ever produced for Corvette. They are painted a light metallic gray, and show off the Z06's red brake calipers, especially when the car is in motion. Each wheel's center cap has a red Corvette crossed-flags emblem for added identification when the car is at rest.
Goodyear has specifically designed new wider, stickier tires for the Z06. Called Goodyear Eagle F1 SC (Supercar) tires, they allow the Z06 to handle, brake and perform better than any production Corvette, ever. Sizewise, the new tires differ from the Goodyear Eagle F1 GS EMT tires on coupes and convertibles as follows: While larger, these tires are much lighter than the EMT tires, reducing mass by a total of 23.4 pounds. The Eagle F1 SC tires have an asymmetric tread pattern to enable the fantastic cornering capabilities of the Z06. With the asymmetric pattern, the outside shoulder of the tire performs well in the dry, while the inside tread performs well in the wet. Taking mass out of the tires is extremely beneficial for wheel control because it reduces unsprung weight. It also reduces rotational mass, which improves acceleration and braking performance. Wheel control on the Z06 is also improved due to the more compliant sidewalls on these new, non-EMT tires. Because these tires do not have the "run flat" capabilities of the EMT tires, it was necessary to develop a process for dealing with tire punctures, since Corvettes do not come equipped with a spare tire. In the case of the Z06, a GM Tire Inflator Kit is included that is capable of sealing punctures up to 5mm in diameter. The kit consists of a squeeze bottle filled with a non-flammable latex compound in an aqueous base, a nozzle that attaches to the tire valve, and a mini air compressor with a 12-volt adapter that plugs into the car's accessory power outlet. The latex compound in the tire inflator kits is not compatible with the tire valves used in Corvette's standard tire pressure monitoring system, so regular tire valves are used and that option is not offered on the Z06. There is a mass reduction of just over a half-pound as a result.
The Z06 receives several other refinements in addition to its unique engine, suspension, wheels and tires that either help it to be more functional or serve to differentiate its appearance, sometimes both.
Having the best of both worlds reduced weight and increased power makes the Corvette Z06 a force to be reckoned with, on or off the track.
Functional air inlets in the center of the front fascia deliver cool air to the intake system. New air scoops on the rear rocker panels funnel air to the rear brakes for better cooling. Z06 rear brake temperatures are reduced by as much as 10 percent under competition conditions. Brake fade and wear are greatly reduced.
Z06 emblems are placed on the front fenders. Front and rear disc brake calipers on the Z06 are painted red. Inside, the Z06 includes a different instrument cluster with stylized graphics and a higher 6500 rpm redline.
The Z06's leather-trimmed seating surfaces include additional side bolstering to hold driver and passenger firmly in place during high lateral load maneuvers, and a Z06 logo is embroidered into the headrests.
You can read more in the following 2 links. The first link is from when the 2001 Z06 was introduced and the second shows the changes for the 2002 model year Z06. The 2003-2004 Z06's were the basically the same as the 2002 except for the shocks in the '04:
2001 Z06 info: http://www.z06vette.com/01.php
2002 thru 2004 Z06 info: http://www.z06vette.com/02.php
2001 thru 2004 Z06 info: http://www.corvetteactioncenter.com/...l#.UbfqaUnD_IU