Anytime the transmission and engine are separated for service (i.e. clutch job, end or transmission rebuild), it is highly recommended to change the pilot bearing, pilot bearing grease seal, and throw-out release bearing.  The stock OEM Mazda pilot bearing is not designed to handle repeated abuse from removing and reinstalling the engine to transmission and vice versa.

When the pilot bearing fails, shifting the transmission into gear will get harder and harder.  After a certain point, it will be next to impossible to shift the transmission into any gear.  The pilot bearing starts to come apart and bits and pieces of the pilot bearing start to bind the transmission input shaft to the eccentric shaft, basically fusing the engine and transmission together.  Due to this binding, this prevents the transmission to synchronize the gears to allow the shifter to select a gear.  If you're able to shift gears with the engine off but unable to do the same with the engine running, this is most likely a dying pilot bearing.  You can sometimes feel the binding of the disintegrating pilot bearing when the engine loads down and wants to die when you're at a stop and the transmission is in neutral or clutch pedal is in; the car will slightly surge forward at the same time the engine bogs down.  After a certain point, the pilot bearing pieces would've all fell out so the binding disappears.  We have seen pilot bearing failures where only the outer case was still intact in the eccentric shaft, and the inner race and all needle bearings were no where to be seen.

Some will argue that it is necessary to use the Mazda SST to remove the pilot bearing.  We have found that a good, aftermarket pilot bearing puller works well.  Brands such as Cornwell and SK make pilot bearing pullers that work fine on this pilot bearing removal job.  We've even used generic pilot bearing pullers purchased from a local tool store (Post Tools in CA) that also worked.  The key to having these tools work is that the end that grips the pilot bearing case needs to be in good shape.  We've heard of horror stories of rented pilot bearing pullers from the local auto parts store that could not do the job, because the jaws were in bad shape.

After pulling the grease seal, make note of the depth of the pilot bearing.

Once you remove the old seal and pilot bearing, just replace with new parts.  It helps to lube the opening in the eccentric shaft with some grease to help the pilot bearing go in easier.  Use an appropriate size socket to tap the pilot bearing into the proper depth.  After tapping the pilot bearing in, grease the pilot bearing itself with more grease.  Insert the pilot bearing seal; use the socket to help tap the seal in if needed.

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