Below is a practical, step‑by‑step procedure for replacing the transmission input shaft on a Toyota 4Runner. I’ll cover tools and consumables, safety, removal and disassembly, how each tool is used, reassembly, common pitfalls, and recommended replacement parts. Use your vehicle’s factory service manual for model/year‑specific fastener locations and torque specs — exact bolts, clearances, and torque numbers vary by year and transmission model.

Important safety first
- Work on a level surface, use wheel chocks.
- Disconnect the negative battery terminal before starting electrical/work.
- Support the vehicle on rated jack stands — never rely on a jack alone.
- Use an engine support bar or jack under the oil pan with a block of wood if you must support the engine when the transmission is removed.
- Wear safety glasses, gloves, and use hearing protection when needed.
- Drain transmission/transfer case/engine fluids into appropriate containers and dispose per regulations.

Tools & equipment (typical)
- Complete metric socket set and wrenches (6–24 mm), extensions and swivel.
- Torque wrench (range to at least 150 ft‑lb).
- Breaker bar.
- Pry bars and large flat screwdrivers.
- Transmission jack or floor jack with a padded block and safety straps.
- Engine support bar or transmission jack and engine support.
- Snap‑ring (circlip) pliers.
- Bearing puller / two‑ or three‑jaw puller.
- Hydraulic press (or arbor press) or bearing driver set.
- Seal driver / appropriate sized sockets.
- Slide hammer (for stubborn seals or bearings).
- Clutch alignment tool (manual) or torque converter alignment guide (auto).
- Impact driver or impact gun (optional).
- Shop rags, brake cleaner, parts trays, marker/labels for hoses/wires.
- RTV/sealant, assembly lube, threadlocker (as specified).

Replacement parts & consumables (recommended)
- Replacement input shaft (OEM or quality aftermarket).
- Input shaft bearing(s) and races (new).
- Bearing retainer/snap rings as required.
- Output/front seals (input seal, rear main seal if disturbed).
- Pilot bearing or bushing (manual) or torque converter pilot (auto) if applicable.
- Gaskets for transmission case halves, pan, transfer case, shift covers as required.
- Transmission fluid and transfer case fluid.
- Clutch kit (disc/pressure/throwout) or torque converter inspection/replace if removed heavily worn.
- Bolts or studs if damaged or single‑use per manual.
- Clean solvent, rags, anti‑seize.

Overview of the work (what you will do)
1) Remove transmission (and transfer case if present) from vehicle.
2) Disassemble transmission/transfer case to access and remove input shaft.
3) Replace shaft plus associated bearings/seals and any worn gears or synchros.
4) Reassemble, reinstall transmission, refill fluids, test.

Step‑by‑step procedure
A. Preparation and vehicle teardown
1. Park vehicle, chock wheels, disconnect negative battery.
2. Jack and support vehicle on stands. Remove any splash shields needed for access.
3. Drain transmission and transfer case fluid into a suitable container.
4. Remove driveshafts / CV axles: mark orientation, unbolt flange/axle nuts, disconnect at transmission/differential hubs, pivot out of the way.
5. Remove exhaust cross‑pipe or mid‑pipe if it interferes with transmission removal.
6. Remove starter motor to access bell housing bolts. Label and set aside.
7. Disconnect electrical connectors, speedometer cable/encoder, shift linkage, transfer case linkage, and any ground straps attached to the transmission. Tag them.
8. Disconnect cooling lines (on automatics) — cap them to limit fluid loss.
9. Support the engine with an engine support or a jack with a block under oil pan (DO NOT lift the engine with oil pan if possible; use proper support).
10. Support the transmission with a transmission jack. Remove transmission crossmember and mount bolts.
11. Remove bell‑housing bolts that attach transmission to engine. For automatics, also remove torque converter bolts through the inspection cover (rotate engine to align bolts). For manuals, remove clutch pressure plate bolts after securing flywheel/clutch.
12. Carefully slide transmission back on the jack until it clears the engine and lower it out of the vehicle. Keep it level.

B. Transmission teardown to remove input shaft
(Exact internal layout differs by transmission. The following is general.)
1. Clean external transmission housing to keep dirt out when opening.
2. Place transmission on a bench on a padded surface. Remove bolts securing case halves or tail housing. Note bolt lengths and locations. Separate case halves/cover. Use a plastic mallet/pry carefully; avoid gouging mating surfaces.
3. Remove shift forks, selector shafts, and linkages as needed to free the main shaft assembly. Keep parts organized and in order.
4. Identify main/input shaft assembly. For manual transmissions, the input shaft usually carries clutch hub and pilot bearing. For automatics, the torque converter input/turbine shaft is integral to the pump — the input shaft may be part of the pump/turbine assembly.
5. Remove snap rings and retaining nuts that hold the input shaft and bearings in place. Use snap‑ring pliers. Keep snap rings oriented correctly — mark the faces if needed.
6. Remove bearings on the input shaft. Use a bearing puller on the bearing outer race or press the shaft out of the bearing depending on design. If shaft and bearing are keyed, press is preferred to avoid damaging journals.
- Tool use: Position two‑ or three‑jaw puller so jaws contact the bearing outer race. Tighten center bolt to extract bearing evenly. If the bearing is stuck, apply penetrating oil and tap the puller gently as you tighten. For heavy presses, use a hydraulic press and appropriate sleeves so force is applied only on the race to avoid damaging the bearing.
7. If the shaft is held in place by gear sets or splines, remove the companion gear, synchro rings, and any thrust washers/bushings as required. Document shim thickness and order.
8. Remove the input shaft out of the case. If it’s tight in the bore, use a press or a puller on the shaft shoulder. Protect splines from damage.

C. Inspect and prepare replacement
1. Clean all mating surfaces, bearings seats, bores and check for scoring, pitting or wear.
2. Inspect gears, splines and synchros. Replace any worn or chipped components. If the bearing race in the case is damaged, replace it.
3. Press new bearings onto the new input shaft using a hydraulic press and bearing driver of the proper diameter — drive on the bearing outer ring only. Use assembly lube on splines as required.
- Tool use: place the shaft on blocks and anvil of press so that force is transmitted to the bearing outer ring. Use a driver or socket that matches the bearing OD. Press slowly and squarely.
4. Install any new snap rings, retaining nuts, and check endplay/shim clearance per the factory spec. If the transmission uses shims for bearing preload or axial clearance, measure and set to specification. Replace worn shims as needed.

D. Reassembly of transmission internals
1. Reinstall the input shaft assembly into the case in reverse order. Ensure gears and synchros engage properly.
2. Reinstall thrust washers, shims, and set endplay. Use dial indicator if required by the manual. Too tight or too loose will cause premature failure.
3. Install snap rings and torque any nuts to spec with a torque wrench. Apply threadlocker if specified.
4. Reassemble shift forks, selector rails, and other internals. Verify smooth operation of shifting mechanism by moving selector shafts.
5. Clean mating surfaces and apply new case gaskets or a bead of specified RTV where required. Reinstall case halves and torque bolts to spec in torque sequence.
6. Reinstall external components (speed sensor, shift linkage) and the transmission mount.

E. Reinstalling transmission into vehicle
1. Place torque converter onto pump (auto) or align clutch assembly (manual) using alignment tool. For automatics, ensure torque converter is fully seated into the pump and engages the torque converter hub and input pump splines—there should be a small clearance then a distinct seating when pushed in. Rotate the converter until bolt holes line up and install bolts finger‑tight first.
2. Lift transmission with the jack and align it to the engine. Carefully slide forward until it engages the dowel pins and bell housing contacts the engine. For manuals, ensure clutch disc is centered with the tool. For automatics, ensure torque converter stays seated.
3. Install bellhousing bolts and torque to spec. Reinstall crossmember, mounts, starter, and reconnect linkage, wiring, and driveshafts per your marks.
4. Refill transmission and transfer case with the correct fluid capacities and type. Check for leaks. Reconnect battery.

F. Final checks and road test
1. With vehicle on stands, start engine and cycle through gears to verify fluid flow and engagement. Check for unusual noises.
2. Lower vehicle and perform a road test. Check shifting, clutch engagement (manual), and for leaks. Re‑check fluid levels after initial warm‑up and a short drive.

Common pitfalls and how to avoid them
- Not supporting the engine: engine can shift and cause damage — always support properly.
- Losing or mixing small parts (snap rings, shims): organize and label parts as removed; use parts trays. Shims determine endplay — mixing causes misassembly.
- Damaging splines or journals: protect splines when using pullers and presses; use correct drivers so force is applied to bearing races only.
- Not replacing bearings and seals: always replace bearings and the input seal when replacing the shaft; reused old bearings often fail quickly.
- Improper seating of torque converter (auto): if not fully seated, bolt holes won’t align or transmission input pump may be damaged. Push converter in until it clicks into place and measure/confirm seating per manual.
- Incorrect torque or reused single‑use bolts: use factory torque specs and replace bolts/studs that are single‑use.
- Contaminants: keep the work area clean and cover open cases to keep debris out.
- Improper endplay/shim settings: measure and set to spec — incorrect preload causes bearing failure and noise.
- Overlooking related wear items: a worn clutch pilot bearing, worn synchros or a damaged tailshaft bearing are often found at the same time. Replace them while you have the transmission open.

Notes on special tools and how they are used
- Transmission jack: supports heavy gearbox and allows controlled lifting/lowering. Strap transmission to the jack to prevent tipping.
- Hydraulic press/bearing driver: used to press bearings on/off the shaft. Use correct sized driver so you press only the bearing race you intend. Press slowly and keep parts square.
- Bearing puller: grips the bearing outer race for extraction. Position puller evenly and tighten center forcing screw to pull bearing. For stuck bearings, apply penetrating oil or heat (controlled) to the case, not the bearing, and use slide hammer if design allows.
- Snap‑ring pliers: compress or spread snap rings for removal/installation. Make sure ring is fully seated in groove.
- Clutch alignment tool: centers the clutch disc so the transmission input shaft slides in easily. Insert tool through clutch into pilot bearing to align before bolting pressure plate.
- Seal driver: a socket or driver of the same OD as the seal pressed squarely into bore to install new seals evenly.

Final recommendations
- Work with a repair manual for your specific 4Runner (year and transmission model) for bolt locations, torque specs and clearances.
- Replace bearings and seals as a set when practical.
- If you don’t have access to a press or are uncomfortable with internal gearbox measurements (endplay/shims), consider a professional rebuild or visiting a transmission shop.
- Keep everything clean and organized; small mistakes are the most common cause of rework.

That’s the complete high‑level and practical sequence. Use factory service manual specs for your model for torque values and tolerances.
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