Harley-Davidson Softail 2006 Service Manual Set (P/N 99482-06)

This three-publication set pairs mechanical repair coverage with the dedicated electrical diagnostic book and the FLSTFSE2 differences supplement.

The supplement is used with the included base manuals. Its fuel-system and fuel-injection sections rely on those books, while its starter section contains specifications only. A drive-section contents note also cites the Touring Models Service Manual, which is not included.

PDF Search, Navigation and Download Contents

Search and diagram detail: Chapter PDFs have searchable text and embedded bookmarks; contents files link the sections. Keep extracted files together. Small wiring labels require zooming. The service manual’s wiring index is offset by two pages; the diagnostics wiring index matches its diagrams.

The ZIP download contains 66 printable PDFs in English, split into chapters, appendices, and contents files. There are 1,197 pages total, including the separate one-page contents sheet and all supplied contents, appendix, notes, and blank pages.

Engine, Chassis and Electrical Service

The following selected coverage highlights outline the repair and diagnostic material. Other included topics cover storage preparation and headlamp alignment.

• Engine repair: Step-by-step procedures for engine removal and installation, top- and bottom-end overhaul, cylinder-head service, cam support plate work, and counterbalancer service.
• Chassis and brakes: Wheel lacing and truing, sealed wheel-bearing replacement, conventional and Springer fork service, steering-head work, brake repair, and bleeding.
• Primary drive and transmission: Clutch inspection, primary-chain and sprocket service, drive-belt replacement, shifter repair, and mainshaft, countershaft, and transmission-case procedures.
• Carburetor and EFI: Carburetor disassembly and adjustment, intake-leak testing, fuel-pump and injector service, induction-module work, and fuel-pressure diagnosis.
• Starting and charging: Starter current-draw tests, solenoid checks, battery testing, voltage-drop diagnosis, and alternator, stator, and regulator troubleshooting.
• Instruments and security: Speedometer self-diagnostics, TSM/TSSM fault charts, key-fob assignment and synchronization, password learn, bank-angle operation, and serial-data fault tracing.
• FLSTFSE2 differences: Model-specific engine specifications, cylinder-head and counterbalancer details, hydraulic clutch service, tachometer diagnosis, and regulator mounting.

It is suited to mechanically qualified owners and technicians who have the proper tools and test equipment; component-level engine, transmission, and electrical work assumes more than beginner maintenance experience.

Mechanical Repair Depth and Variant Differences

The base manual covers the Softail Standard, Night Train, Deuce, Springer, Heritage, Fat Boy, Deluxe, and Springer Classic range, including Shrine FLSTFI and FLSTCI versions. Model-specific procedures distinguish conventional and Springer front ends, with applicable wheel, brake, fender, seat, console, tail-lamp, and exhaust arrangements.

Engine service planning: The engine section separates work that can be performed in the chassis from repairs requiring engine removal and crankcase separation. These service paths help establish the teardown scope before work begins. Detailed sections address oil flow and pressure diagnosis, valves and guides, pistons, connecting rods, crankcase bearings, camshafts, and the oil pump.

Flywheel/connecting-rod coverage provides inspection criteria and assembly replacement rather than internal flywheel rebuilding. The transmission material includes shifter-cam and fork service, shaft disassembly and assembly, case repair, and a separate Japan-only mainshaft/countershaft procedure.

Fault Charts, Wiring Diagrams and Test Equipment

The diagnostic volume explains check-engine and security-lamp behavior, speedometer initialization, current versus historic trouble codes, and Digital Technician HD-44750 use. Factory charts trace no-crank, no-start, start-then-stall, misfire, sensor, relay, fuel-pressure, and communication faults, including B1004/B1005 instrument faults and U1300/U1301 “BUS Er” conditions.

Speedometer self-diagnostics can retrieve and clear codes; distinguishing current from historic codes requires Digital Technician. Post-replacement TSM/TSSM configuration and password-learning requirements are also documented.

Circuit-level support: The same 20 indexed wiring diagrams appear in both base publications. Examples 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 diagrams.

Connector-number tables, pin locations, harness routing, terminal removal, sealed-splice repair, breakout-box checks, and wiggle tests support fault isolation. Connector procedures cover Multilock, Deutsch, Mini-Deutsch, Delphi, and Packard designs.

FLSTFSE2 Engine and Hydraulic Clutch Details

The supplement documents cylinder-head and valve work, rocker housings, cylinder boring and honing, cam timing marks, and the counterbalancer’s roller-bearing and thrust-washer arrangement. Its tapered connecting rods have nonserviceable piston-pin bushings; the specified replacement is a complete flywheel assembly.

Hydraulic clutch material extends to master-cylinder rebuilding, fluid-line replacement and bleeding, secondary-actuator rebuilding, and release-bearing and pushrod service. The supplement specifies DOT 4 fluid and warns that incompatible fluid can damage the clutch system.

Workshop References and Repair Cautions

Assembly-specific torque tables, service wear limits, fits and clearances, fluid data, wheel and belt specifications, brake and clutch data, and electrical test values accompany the procedures.

The illustrated tool appendix identifies 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.

For Japan-only transmission work, incorrect retaining-ring positioning during shaft pressing can damage gear teeth; the main-drive-gear procedure also identifies the installation tooling needed to prevent premature bearing failure.

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.

Selected Fuel-Pressure and Clutch-Travel Checks

EFI fuel pressure: The running-engine test specifies a steady 55–62 psi (380–425 kPa) as engine speed changes. Its diagnostic chart distinguishes low, high, and steady pressure conditions and directs checks toward restrictions, pump delivery, internal leakage, or the regulator.

FLSTFSE2 hydraulic clutch: The release-bearing procedure specifies at least 0.065 in. (1.65 mm) of axial pushrod and release-plate movement when the clutch lever is actuated. This measurement supports the hydraulic-system check after clutch service and bleeding.