1998–2002 Yamaha WR400F / WR426F Service Manual (P/N 5NG-28199-30)

• Covers Yamaha WR426F(N) and WR400F(N) competition off-road configurations identified in the factory publication, including WR426FN (USA/5NG1), WR426F (Europe/5NG2), WR426F(N) (CDN, AUS, NZ, ZA/5NG4), WR400F (Europe), and WR400FN (AUS), model code 5GS9.
• Official OEM publication — Yamaha reference 5NG-28199-30.
• 758-page multilingual OEM PDF with English technical content presented alongside French, German, and Spanish sections.

Factory Workshop Reference

When you have a top end torn apart on the bench, the useful information is model-specific: dimensions, service limits, fastener data, special tools, and the correct removal, inspection, and assembly sequence. This factory publication breaks the WR down across seven chapters: General Information, Specifications, Regular Inspection and Adjustments, Engine, Chassis, Electrical, and Tuning.

On the engine side, the manual covers sequential repair procedures for the KEIHIN FCR-MX39 carburetor, camshafts, cylinder head, valves and valve springs, cylinder and piston, separate WR426F and WR400F clutch assemblies, oil filter, water pump, right crankcase cover, balancer, trochoid oil pump, kick axle and shift shaft, CDI magneto, engine removal, crankcase and crankshaft, and transmission/shift cam/shift fork assemblies. These are not inspection summaries. The repair sections identify extent of removal, replacement criteria, service limits, special-tool requirements, assembly notes, lubricant and locking-agent callouts, and tightening data.

The shop-level procedure coverage includes valve-clearance adjustment with pad-selection tables; camshaft, timing-chain, cylinder-head, valve, and piston repair; clutch overhaul; engine removal and crankcase separation; crankshaft removal and installation; transmission and shift-fork inspection; front-fork disassembly, seal, and oil service; steering-head, swingarm, and linkage bearing work; brake caliper and master-cylinder service with brake-system bleeding; coolant and engine-oil/filter/strainer service; and ignition/TPS fault tracing. Yamaha also identifies purpose-built tooling such as the YU-1135-A / 90890-01135 crankcase separating tool, YU-33270-B / 90890-01362 flywheel puller, YM-01442 / 90890-01442 fork seal driver, YM-04019 / 90890-04019 valve spring compressor, YM-91042 / 90890-04086 clutch holding tool, and YU-3112-C / 90890-03112 pocket tester.

Electrical coverage goes well beyond a generic wiring page. The map-controlled CDI unit uses engine-speed and TPS input to determine ignition timing, while dedicated diagnostic sections cover the ignition system, CDI magneto, ignition coil, TPS, neutral switch, and lighting system. TPS coil resistance is specified at 4–6 kΩ at 20°C (68°F); WR426F CDI units are identified as 5NG-00 for USA and 5NG-10 except USA, while the WR400F uses 5GS-60. Carburetor tuning data includes a #165 main jet, #42 pilot jet, 8 mm float height, 1,700–1,900 r/min idle speed, and 33.3–38.7 kPa (250–290 mmHg) intake vacuum, with WR426F OBDRR-4 / OBDQR-4 and WR400F OBDRQ-4 jet-needle specifications.

Reference material named in the manual includes the lubrication diagrams, cable routing diagram, electrical components and wiring diagram, lighting-system inspection flow chart, valve-clearance pad selection tables, and carburetor setting-by-symptom chart. Removal and disassembly sections are also built around exploded diagrams and job instruction charts, tying component identification to work order and extent of removal.

Critical Specifications and Safety

The documentation goes deep into the technical details required for professional bench work. Both engines use a 12.5:1 compression ratio, but they do not share every dimension: the WR426F bore × stroke is 95.0 × 60.1 mm, while the WR400F is 92.0 × 60.1 mm. Cold valve clearance is 0.10–0.15 mm intake and 0.20–0.25 mm exhaust. The cylinder-head warp limit is 0.05 mm, while piston-to-cylinder clearance is 0.040–0.065 mm with a 0.10 mm service limit.

Need to verify the clutch pack? The existing 48.4 mm clutch spring free length applies specifically to the WR426F, which uses six clutch springs. The WR400F specification is 44 mm with five springs, and its friction-plate arrangement and wear limits are different as well. That model separation matters during repair work because values from one WR clutch cannot simply be carried over to the other.

Fluid and chassis data is equally specific. Engine oil capacity is 1.5 L (1.59 US qt) for a periodic change, 1.6 L (1.69 US qt) with oil-filter replacement, and 1.7 L (1.80 US qt) total; coolant capacity including all routes is 1.2 L (1.27 US qt). Front-fork data specifies Suspension oil “01” with 573 cm³ (19.4 US oz) / 135 mm oil level for USA, CDN, AUS, NZ, and ZA versus 583 cm³ (19.7 US oz) / 125 mm for Europe. Rear-shock enclosed gas pressure is 1,000 kPa (142 psi). Brake fluid is DOT #4, drive-chain slack is 40–50 mm (1.6–2.0 in), and front/rear tire pressure is 100 kPa (15 psi).

Torque tables make the repair data usable at the bench rather than merely descriptive. Examples include the spark plug at M10S × 1.0 / 13 Nm (9.4 ft-lb), clutch boss at M20 × 1.0 / 75 Nm (54 ft-lb), front axle at M16 × 1.5 / 105 Nm (75 ft-lb), rear axle at M20 × 1.5 / 125 Nm (90 ft-lb), and frame oil strainer at M18 × 1.5 / 90 Nm (65 ft-lb). The lubrication section also traces the dry-sump system through the oil tank, oil strainer, trochoid oil-pump rotors, oil filter and check ball, cylinder head, crank pin, piston pin, camshaft, valve lifter, main axle, drive axle, and transmission gears.

Several repair traps called out by Yamaha are easy to miss. Crankcase fasteners are treated as a controlled sequence because uneven release or tightening can load the case mating surfaces; the crankshaft is specifically not to be driven out with a hammer. In the rear suspension linkage, incorrect connecting-rod nut orientation can cause the nut to contact the swingarm as the rear shock moves through its stroke.

Please keep in mind that working on high-performance competition machines carries inherent risks. Always double-check your fastener management—like the 13 Nm spark plug torque specification—and ensure you are operating with the correct tools in a safe shop environment. The reference figures provided here highlight the depth of the manual, but qualified mechanics should always rely on the full OEM documentation as the authoritative source before starting any mechanical work.