What this repair is, why it’s needed, and how the system works (plain-English theory)
- What the “input shaft” is: on a Jeep TJ the input shaft I’ll describe is the shaft in the transfer case that receives rotation from the transmission (sometimes called the transfer‑case input shaft). Think of it as the short coupling shaft that takes power out of the transmission and hands it to the transfer case. Analogy: it’s like the little coupling on a bicycle that connects the pedal crankset to the chainring assembly — if the coupling splines or bearings wear, power won’t pass cleanly and you get noise, play, slipping or complete loss of drive.
- How the system works: the engine → transmission output flange → transfer‑case input shaft → transfer‑case internal gears/chains → front/rear outputs → driveshafts → axles/wheels. The input shaft’s splines and bearings align and carry torque into the transfer case. It also usually passes through or seats a seal to keep transfer case fluid in.
- Why you’d replace it: symptoms include loud/metallic whining or crunching from between transmission and transfer case, excessive play at the transmission-to-transfer case joint, metal flakes in transfer case fluid, fluid leaks at the input seal, and intermittent/no power to front/rear output. Causes: worn splines, damaged/flat‑spotted bearings, a failed snap ring, corrosion, or a scored shaft/seal that leaks. If you ignore it you can score mating parts inside the transfer case and damage gears, bearings and seals — making a small repair into a full rebuild.
- What can go wrong during/after the repair if done wrong: incorrect bearing/seal installation leading to leaks; wrong snap‑ring placement or missing circlips causing shaft walk and catastrophic failure; improper bearing preload or endplay causing premature wear and noise; misaligned transfer case causing vibration; loose bolts causing separation; contamination leading to early failure.

Overview of components you will see and what each does
- Transfer case housing/case: holds gears, bearings, shafts and fluid.
- Input shaft (transfer case): transfers torque from the transmission output to internal gears; has splines for mating with transmission output flange.
- Bearings (roller or ball bearings, sometimes a pilot bearing): support the input shaft radially and (in part) axially.
- Bearing races/shims/crush sleeve (if present): set preload/endplay for bearings.
- Snap rings/circlips: retain the shaft in the case.
- Input seal (shaft seal): keeps fluid in the case where the shaft exits the housing.
- Output gears/chain (internal): receive power from the input shaft and send it to outputs.
- Transfer case-to-transmission bolts and dowel pins: align and secure the two housings.
- Speedometer sensor/gasket/shifter linkage (if present): attachments that must be removed.
- Yoke or slip yoke: connects the transfer case output to the driveshaft; you will remove driveshafts to access the case.

Tools, supplies, and workspace prerequisites
- Service manual for your exact TJ year/model and transfer case (pull charts, torque specs, shims, sequences).
- Clean, flat workspace and quality jack stands (never rely on a jack).
- Transmission jack or floor jack + block to support transfer case/transmission.
- Basic hand tools: metric sockets, ratchet, extensions, combination wrenches.
- Impact or torque wrench (calibrated).
- Snap‑ring pliers, bearing puller/puller set, drift punches, hammer.
- Hydraulic press (or access to a shop press) for bearing & shaft install.
- Seal driver or correct diameter socket, soft mallet.
- Pry bars, gasket scraper, brake cleaner/parts cleaner, rags.
- New parts: replacement input shaft (OEM or quality aftermarket), bearings & races, seals, snap rings, any shims/dowels that are worn, transfer case gasket or RTV, bolts (replace if damaged), transfer case fluid.
- Thread locker (per manual), anti‑seize for some bolts (per manual), assembly lube or high‑temp grease.
- Safety gear: gloves, eye protection.

Preparation and safety (read every step)
- Park level, block wheels, disconnect battery for safety.
- Raise vehicle and support on jack stands with generous clearance around transfer case. Use a transmission jack or second floor jack to support the transfer case and transmission before any unbolting.
- Label and photograph wire connectors, vacuum lines, linkages, driveshaft orientation marks and bolt patterns so you can reinstall exactly the same way. Note the rotational orientation of the transfer case relative to the transmission — you must preserve alignment.

Step-by-step procedure (high level then detailed steps)
High-level: remove driveshafts → drain transfer case fluid → disconnect shift linkage and sensors → support transfer case and separate from transmission → remove input shaft and associated bearings/seal → inspect internal parts → install new shaft with new bearings/seals and correct retention (snap ring/shims) → reassemble, torque to spec, refill fluid and test.

Detailed steps
1) Remove driveshafts and peripherals
- Mark driveline orientation (paint or tape) so you can reinstall exactly as before.
- Remove front and rear driveshafts at yokes (4-bolt or 2-bolt, depending). Set aside.
- Remove transfer case skid plate if fitted, and any crossmembers interfering.
- Disconnect shift linkage, speedo sensor, vacuum lines, electrical connectors, vent hoses. Cap lines to avoid contamination.

2) Drain fluids
- Place drain pan under transfer case and remove drain plug and fill plug to speed draining.
- Remove bolts and note bolt locations.

3) Support transmission and transfer case
- Place a transmission jack or floor jack under the transfer case and also support the transmission output flange so no load is on the bolts when you unbolt the case. Transmission must be supported before separating.

4) Separate transfer case from transmission
- Loosen and remove transfer case-to-transmission bolts. There may be dowel pins; the case will hang on those — remove bolts gradually while supporting transfer case. Gently separate the case from the transmission; you may need to rotate the output flange to free it from splines. Be careful not to let the transfer case drop.
- Inspect the transmission output flange and transfer case mating surface for damage.

5) Remove the input shaft assembly
- With the transfer case on a bench, drain remaining fluid and clean the exterior.
- Remove any internal retainer bolts, shims, or covers that block input shaft removal (follow manual order). Note that some models have internal snap rings accessed by removing rear cover or side cover.
- Use snap‑ring pliers to remove circlips that retain the input shaft.
- Press out bearings or use a bearing puller to remove bearings from the shaft if they remain. In some cases you will press the shaft out of the case carrying bearings; in others the bearings stay in the case — follow your model’s disassembly flow.
- Carefully remove the shaft, watching for shims, spacers, washers, and note exact order and orientation. Lay out parts in the order removed or photograph/label them. Replace any worn or pitted components.
- Clean the shaft bore and internal surfaces; remove any metal flakes — contamination is a primary cause of future failure.

6) Inspect all internal components
- Check mating splines on transmission output flange and transfer case input shaft for wear, deformation or rounding. If splines are chewed you may need to replace the flange or transmission output shaft.
- Inspect bearing races for pitting; replace bearings and races as a matched set if any wear is found.
- Inspect gears and chain (if chain case) for chipped teeth or excessive wear.
- Replace seal bores or install fresh seal if scored.

7) Prepare new parts
- Compare new shaft to old to ensure correct length, spline count and keyways.
- Install new bearings onto new shaft with a press using the proper race surfaces. Don’t press on the bearing inner race if pressing onto a shaft where that would damage rollers; use correct driver and method.
- Install any new snap rings/circlips, spacers and shims exactly as removed. Some transfer cases use a specific shim stack to set endplay — measure and restore endplay to spec (factory manual).

8) Install input shaft
- Lightly lube splines with assembly lube; slide shaft into the case, install circlips/snap rings in the correct grooves; ensure they fully seat.
- Verify radial seating and bearing arrangement. If bearings have preload or shims, set these now (consult manual). If your case uses a crush sleeve or shims, follow the factory procedure to get correct endplay.

9) Install seals
- Install new input seal using a seal driver so it seats squarely at correct depth. A crooked seal will leak quickly.

10) Reassemble transfer case and mate to transmission
- Clean the mating surfaces; use new gasket or RTV as recommended by the manual.
- Lift the transfer case into position on the transmission, guiding dowel pins and splines carefully so nothing is forced. If it does not slide in easily, back off and recheck alignment — forcing will damage splines and the new seal.
- Tighten transfer case bolts finger‑tight first in a cross pattern, then torque to spec in sequence. Apply thread locker where the manual specifies. Replace any dowel pins if worn.

11) Reinstall driveshafts and peripherals
- Reattach shift linkage, sensor connectors, vent hoses, and driveshafts using the orientation marks you made.
- Reinstall skid plates or crossmembers.

12) Fill & test
- Fill the transfer case with the correct type and quantity of fluid specified by the factory manual.
- Before lowering, rotate driveline by hand (with parking brake on and wheels blocked) and shift transfer case through ranges to check for binding.
- Lower vehicle, reconnect battery, start engine and, with the vehicle safely supported, check for leaks.
- Road test at low speed first: test 2WD, 4WD part-time modes, listen and feel for vibration, whining, clunking. Recheck fluid level and fasteners after short drive.

Important measurements and tolerances (what to verify)
- Bearing preload or endplay: many transfer cases specify a small axial endplay for the input shaft (measured with a dial indicator). If endplay is too large, the shaft will walk and cause noise; too tight and bearings will overheat. Exact numbers vary by model — consult the factory manual and set to specification with shims or crush sleeve.
- Snap ring seating: must be fully engaged in groove to retain shaft.
- Seal depth: must be flush or at manufacturer-specified depth.
- Bolt torque: use factory spec for transfer case bolts and any accessory bolts.

Common pitfalls and troubleshooting
- Forcing parts together: if the transfer case won’t mesh onto the transmission splines, do not force it — the splines or new seal will be damaged. Rotate the transmission output slightly to align splines and use dowel pins to align.
- Reusing old seals or bearings: bad idea — always replace bearings and seals if you’ve opened the case.
- Missing or reversed shims: will change endplay and cause premature failure.
- Contamination: metal flakes in fluid or dirt on components will destroy bearings rapidly — keep everything clean.
- Not supporting the transmission: the weight can shift and break bolts or damage housings.
- Not checking the transmission output flange/splines: a worn transmission flange will quickly wear a new transfer-case shaft; replace both if needed.
- Over/under torque: incorrect bolt torque can cause distortion or separation; always use torque wrench and factory values.

Final checks and advanced tips
- After a few hundred miles, recheck bolts and fluid level.
- If noise persists: check for worn transmission output shaft, check pilot bearing (if present), and check for internal gear damage — noise may not originate at the input shaft alone.
- If you’re uncomfortable with press work (bearing removal/install) or setting preload/endplay, it’s appropriate to use a shop for that portion — it’s easy to ruin bearings by improper pressing.
- Keep notes and photos. Reassembly will go much faster and correctly if you have a photographic record.

Torque and spec note
- Exact torque values, endplay/preload, shim sizes and seal depths vary by transfer case model (NP231, NP242, etc.) and year. The procedure above covers the mechanical steps and inspection points, but you must use the Jeep factory service manual or a reputable shop manual for the precise numbers and any model‑specific steps.

Safety reminder
- Always use jack stands, eye protection and clean work practices. If any step (pressing bearings, measuring preload) is unfamiliar, consider a professional for those operations.

That’s the complete beginner‑level procedure and theory in one place. Follow the manual for torque and tolerance values, replace bearings and seals whenever you open the case, and take your time aligning parts — careful measurement and cleanliness are what make this job last.
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