Yamaha YZF-R6 1999–2002 Service Manual (P/N 5EB1-AE1)

Yamaha's first-edition YZF-R6 '99 service manual, dated August 1998 and identified on the cover as 5EB1-AE1, is supplied as a 400-page PDF. It covers the 1999 5EB launch model only - the liquid-cooled, four-stroke DOHC inline-four with a six-speed constant-mesh transmission - rather than the entire 1999-2002 series. Yamaha produced this manual primarily for its dealers and qualified mechanics; anyone using it for maintenance or repair is expected to already understand motorcycle mechanics and repair techniques.

• Engine and transmission repair: Covers engine removal, camshaft and cylinder-head work, valve and valve-spring service, piston and connecting-rod inspection, crankshaft bearing selection, crankcase assembly, oil-pump service, clutch repair, and transmission inspection.
• CVRD37 carburetors and fuel delivery: Details carburetor removal, separation, inspection, reassembly, synchronization, fuel-level adjustment, throttle-position-sensor adjustment, and fuel-pump and fuel-cock testing. The specification table distinguishes 5EB00, 5EB200 (G), and 5EB300 (F) carburetor ID marks.
• Cooling-system procedures: Includes radiator and cap testing, oil-cooler inspection, thermostat checks, and water-pump removal, disassembly, seal installation, reassembly, and installation.
• Wheel and brake service: Provides front- and rear-wheel removal and installation, bearing and brake-disc inspection, static balancing, pad replacement, master-cylinder and caliper service, and hydraulic brake bleeding.
• Suspension, steering, and final drive: Documents telescopic-fork removal and rebuild, spring-preload plus rebound- and compression-damping adjustment, steering-head service, rear-shock and linkage inspection, swingarm work, and drive-chain replacement and adjustment.
• Electrical diagnosis: Uses circuit diagrams and fault-isolation checks for the CDI ignition, starting-circuit cutoff system, starter motor, AC magneto charging system, lighting, signaling, cooling fan, fuel pump, and tachometer-based self-diagnosis for the throttle position sensor and fuel-level indicator.

Engine Overhaul and 5EB Service Details

Removal and disassembly sections open with exploded views and ordered job charts, then continue into inspection and reassembly requirements. The engine overhaul material goes beyond routine tune-up work: it addresses cam timing, valve-seat and guide checks, cylinder and piston wear, connecting-rod and crankshaft bearing clearances, lubrication passages, shift forks, the shift drum, and individual transmission gears. Periodic service sections add valve-clearance adjustment, carburetor synchronization, compression and oil-pressure testing, ignition-timing checks, cooling-system service, steering-head adjustment, and chassis lubrication.

The suspension content includes the factory adjusting positions for front and rear spring preload, rebound damping, and compression damping. The rear shock chapter is narrower than the fork chapter: it covers handling, removal, inspection, installation, and disposal of the nitrogen-charged shock and gas cylinder, but not an internal shock rebuild.

Wiring, Yamaha Tools, and Factory Data

Named visual references include oil-flow diagrams, coolant-flow diagrams, cable-routing views, the starting-circuit cutoff operation schematic, throttle-position-sensor and fuel-level self-diagnosis circuits, and complete YZF-R6 '99 wiring diagrams for Europe and Australia. Exploded assembly views support the mechanical repair chapters throughout the manual.

The special-tool section identifies each Yamaha tool by number and function. Examples include the fork spring compressor 90890-01441, fork seal driver and attachment 90890-01376 / 90890-01374, vacuum gauge and adapter 90890-03094 / 90890-03060, clutch holding tool 90890-04086, and ignition checker 90890-06754. Factory reference tables provide component-specific tightening torques, fluid capacities, approved lubricants, inspection limits, clearances, adjustment data, and electrical test specifications.

5EB-Specific Repair Cautions

The engine repair notes warn that moving the crankshaft during camshaft installation can cause damage or incorrect valve timing, and that big-end and main-journal bearings must remain in their matched positions. The fork's damper-adjusting internals are particularly sensitive to contamination. Hydraulic brake work, the hot pressurized cooling system, and the nitrogen-charged rear shock require the manual's safety procedures; incorrect service can damage components or leave the motorcycle unsafe.