Harley-Davidson Softail Fat Boy, Springer, Night Train 2006 Service Manual (P/Ns: 99482-06, 99494-06, 99498-06)

• 1,197 PDF pages total - Service Manual P/N 99482-06: 680 pages; Electrical Diagnostics P/N 99498-06: 402 pages; FLSTFSE2 Service Supplement P/N 99494-06: 114 pages; separate contents sheet: 1 page.
• Coverage spans 2006 Softail Standard, Night Train, Deuce, Springer, Heritage, Fat Boy, Deluxe, and Springer Classic models in carbureted and EFI form, plus the FLSTFSE2 Screamin' Eagle Fat Boy.
• Engine repair material covers engine removal and installation, top- and bottom-end overhaul, cylinder-head service, cam support plate and oil-pump work, and counterbalancer assembly.
• Chassis and driveline procedures include wheel lacing and truing, conventional and Springer fork service, brake repair and bleeding, clutch and primary-drive work, belt replacement, and transmission overhaul.
• Electrical fault finding follows the factory test paths for starter current draw and solenoid operation, alternator/stator and regulator output, ignition coils, instruments, TSM/TSSM security, carbureted ICM systems, and EFI engine management.
• Wiring support includes connector locations and terminal repair for Multilock, Deutsch, Mini-Deutsch, and Packard connectors, plus 20 indexed carbureted/EFI wiring diagrams with model- and market-specific circuits.

This three-publication set pairs mechanical repair coverage with the dedicated electrical diagnostic book and the FLSTFSE2 differences supplement. It is suited to mechanically qualified owners and technicians who have the proper tools, service data, and test equipment; component-level engine, transmission, and electrical work assumes more than beginner maintenance experience.

Model and Repair Coverage

The base manual's VIN table identifies FXST/FXSTI, FXSTB/FXSTBI, FXSTD/FXSTDI, FXSTS/FXSTSI, FLST/FLSTI, FLSTC/FLSTCI, FLSTF/FLSTFI, FLSTN/FLSTNI, and FLSTSC/FLSTSCI models, including Shrine FLSTFI and FLSTCI versions. It distinguishes carbureted and fuel-injected Twin Cam 88B configurations, domestic and international markets, and California applications. Model-specific sections account for conventional and Springer front ends and the applicable wheel, brake, fender, seat, console, tail-lamp, and exhaust arrangements.

Beyond scheduled service, the engine chapters cover oil-flow and pressure diagnosis, cylinder-head and valve work, pistons and connecting rods, camshafts, crankcase bearings, and flywheel repair. Transmission coverage includes shifter-cam and fork service, mainshaft and countershaft disassembly, and case repair. An appendix identifies Japan-only transmissions by a third digit of 9 in the eight-digit case code and provides the different shaft procedure used for that build.

Instrument and Electrical Diagnostics

The diagnostic volume explains check-engine and security-lamp behavior, speedometer initialization, current versus historic trouble codes, speedometer self-diagnostics, and Digital Technician HD-44750 use. Factory charts isolate no-crank, no-start, start-then-stall, misfire, charging, fuel-pressure, sensor, relay, and serial-data faults. DTC coverage extends from B1004/B1005 instrument faults and P-series ICM/ECM faults to U1300/U1301 "BUS Er" communication errors. Password learn, key-fob assignment and synchronization, bank-angle operation, and post-replacement TSM/TSSM setup are also documented.

The same 20 indexed wiring sheets appear in both the service-manual appendix and the diagnostics wiring section. Representative diagrams include the Carbureted Main Harness, Carbureted Charging & Starting Circuits, three-sheet EFI Main Harness, EFI Horn & Instruments, EFI Ignition Circuit, and two-sheet Security Circuit. Connector-number tables, pin locations, harness routing, terminal removal, sealed-splice repair, breakout-box checks, and wiggle tests support circuit-level diagnosis.

FLSTFSE2-Specific Content

The supplement covers the FLSTFSE2's 103 cu. in. (1690 cc) fuel-injected, balanced engine and the parts that differ from the base Softail build. Unique chapters address cylinder heads and valve work, rocker housings, cylinder boring and honing, cam timing marks, counterbalancer details, wheels and controls, tachometer diagnosis, regulator mounting, and the hydraulic clutch master cylinder, fluid line, secondary actuator, release bearing, and pushrod.

This is a differences-only supplement. Its fuel-system section contains no unique procedure and its starter section contains specifications only, while fuel-injection and electrical work refers to the included base manuals. The drive section points to the Touring Models Service Manual for non-supplemental clutch-release-bearing information; that publication is not included.

Specification and Reference Data

The manuals provide assembly-specific torque tables, service wear limits, fits and clearances, fluid data, wheel and belt specifications, brake and clutch data, pressure-test specifications, and carbureted/EFI-specific electrical test values. The illustrated tool appendix identifies equipment by part number, including the carbureted Breakout Box HD-42682, EFI Breakout Box HD-43876, Fuel Pressure Gauge HD-41182, Main Drive Gear Remover/Installer HD-35316-B, and Springer Steering Stem Bearing Tool HD-47255.

The Japan-only transmission procedure warns that an incorrectly positioned retaining ring during shaft pressing can put gears into hard contact and damage their teeth; the main-drive-gear procedure calls for the specified installation tool to prevent premature bearing failure. For the FLSTFSE2 hydraulic clutch, the supplement specifies DOT 4 and warns that incompatible fluid can damage the system. Battery and starter testing involves high-current circuits, while EFI fuel testing exposes pressurized gasoline, so the manual's isolation, ventilation, and fire-safety precautions remain part of the job.