I was hoping I wouldn't see any issues with gearboxes on the WRX but it seems it's unavoidable.

Car will no longer shift into 3rd while shifting at normal speeds.
At low speeds and stopped it will go in but massive shifter vibrations and very difficult to get out of gear.

1&2, 4&5 seem fine.

Any ideas on what I should be looking at or expecting to fix.

Might be off to Doug ASAP. PITA to drive w/o 3rd.

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MY00 WRX. 89 Prelude. 99 CRV

possible bent selector fork due to broken teeth. similar thing happened to me

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1997 green GC8 with the usual mild mods.

Is there any noise when its in third? clunking or knocking?

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Its just the internet dude, its not real.
F.B. Racing
01 WRX (STI badged)
2010 XR5 Focus
06 Impreza Hatch 2.0i

No noise from the gear set. Gears run smooth. It's just the selector that vibrates and struggles to engage.

Could well be the fork.

If this is the case is it a gearbox out and rebuild job? or fix while in the car?

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MY00 WRX. 89 Prelude. 99 CRV

It may be the fork, more likely a damaged synchro ring.
Take it to your workshop, they'll know as soon as they drive it.
Either way, synchro or shift fork, its a complete dismantle/rebuild job.

__________________
Its just the internet dude, its not real.
F.B. Racing
01 WRX (STI badged)
2010 XR5 Focus
06 Impreza Hatch 2.0i